Attribute Details

Structure Attributes

ID(s) and Keywords
PDB ID(s)
Attributercsb_entry_container_identifiers.entry_id
DescriptionEntry identifier for the container.
Typestring
Examples
1KIP
4HHB
Iterabletrue
PDB Deposit Group ID(s)
Attributepdbx_deposit_group.group_id
DescriptionA unique identifier for a group of entries deposited as a collection.
Typestring
Examples
G_1002119
G_1002043
Iterabletrue
PDB Assembly ID(s)
Attributercsb_assembly_container_identifiers.assembly_id
DescriptionAssembly identifier for the container.
Typestring
Examples
1
5
PubMed ID
Attributercsb_pubmed_container_identifiers.pubmed_id
DescriptionUID assigned to each PubMed record.
Typeinteger
Minimum Value5
Maximum Value35545671
Examples
15937111
Iterabletrue
EMDB ID(s) for Maps Used in Structure Modeling
Attributercsb_entry_container_identifiers.emdb_ids
DescriptionList of EMDB identifiers for the 3D electron microscopy density maps used in the production of the structure model.
Typestring
Examples
EMD-21578
EMD-30168
Iterabletrue
EMDB ID(s) for Related Maps
Attributercsb_entry_container_identifiers.related_emdb_ids
DescriptionList of EMDB identifiers for the 3D electron microscopy density maps related to the structure model.
Typestring
Examples
EMD-21578
EMD-30168
Iterabletrue
Accession Code(s) - UniProt
Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession
DescriptionReference database accession code
Typestring
Nested Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name
Nested Attribute Examples
P01308
P0CX43
Accession Code(s) - GenBank
Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession
DescriptionReference database accession code
Typestring
Nested Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name
Nested Attribute Examples
12057205
1329886537
Accession Code(s) - NORINE
Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession
DescriptionReference database accession code
Typestring
Nested Attributercsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name
Nested Attribute Examples
NOR00033
NOR00972
Structure Keywords
Attributestruct_keywords.pdbx_keywords
DescriptionTerms characterizing the macromolecular structure.
Typestring
Examples
DNA
RNA
T-RNA
DNA/RNA
RIBOZYME
PROTEIN/DNA
PROTEIN/RNA
PEPTIDE NUCLEIC ACID
PEPTIDE NUCLEIC ACID/DNA
DNA-BINDING PROTEIN
RNA-BINDING PROTEIN
UniProt Molecule Name
Attributercsb_uniprot_protein.name.value
DescriptionName that allows to unambiguously identify a protein.
Typestring
Examples
Hemoglobin alpha
Additional Structure Keywords
Attributestruct_keywords.text
DescriptionKeywords describing this structure.
Typestring
Examples
Inhibitor, Complex, Isomerase...
serine protease
inhibited complex
high-resolution refinement
Entry Group ID(s)
Attributercsb_entry_group_membership.group_id
DescriptionA unique identifier for a group of entries
Typestring
Examples
G_1001001
Polymer Entity Group ID(s)
Attributercsb_polymer_entity_group_membership.group_id
DescriptionA unique identifier for a group of entities
Typestring
Examples
1_100
P00003
Deposition
Structure Title
Attributestruct.title
DescriptionA title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others.
Typestring
Examples
T4 lysozyme mutant - S32A
Rhinovirus 16 polymerase elongation complex (r1_form)
Crystal structure of the OXA-10 W154A mutant at pH 9.0
Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase
Crystal structure of xylanase from Trichoderma longibrachiatum
Structure Author
Attributeaudit_author.name
DescriptionThe name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Typestring
Examples
Jones, T.J.
Bleary, Percival R.
O'Neil, F.K.
Van den Bossche, G.
Yang, D.-L.
Simonov, Yu.A
Structure Author ORCID
Attributeaudit_author.identifier_ORCID
DescriptionThe Open Researcher and Contributor ID (ORCID).
Typestring
Examples
0000-0002-6681-547X
Deposit Date
Attributercsb_accession_info.deposit_date
DescriptionThe entry deposition date.
Typestring
Minimum Value8/10/1972
Maximum Value5/9/2022
Examples
2020-07-11
2013-10-01
Release Date
Attributercsb_accession_info.initial_release_date
DescriptionThe entry initial release date.
Typestring
Minimum Value5/18/1976
Maximum Value5/17/2022
Examples
2020-01-10
2018-01-23
Revision Date
Attributercsb_accession_info.revision_date
DescriptionThe latest entry revision date.
Typestring
Minimum Value11/7/2000
Maximum Value5/17/2022
Examples
2020-02-11
2018-10-23
Structural Genomics Project Name
Attributepdbx_SG_project.project_name
DescriptionThe value identifies the Structural Genomics project.
Typestring
Enumeration
Enzyme Function Initiative
NIAID, National Institute of Allergy and Infectious Diseases
NPPSFA, National Project on Protein Structural and Functional Analyses
PSI, Protein Structure Initiative
PSI:Biology
Examples
PSI, Protein Structure Initiative
Structural Genomics Project Center Initials
Attributepdbx_SG_project.initial_of_center
DescriptionThe value identifies the full name of center.
Typestring
Enumeration
ATCG3D
BIGS
BSGC
BSGI
CEBS
CELLMAT
CESG
CHSAM
CHTSB
CSGID
CSMP
GPCR
IFN
ISFI
ISPC
JCSG
MCMR
MCSG
MPID
MPP
MPSBC
MPSbyNMR
MSGP
MSGPP
MTBI
NESG
NHRs
NPCXstals
NYCOMPS
NYSGRC
NYSGXRC
NatPro
OCSP
OPPF
PCSEP
PSF
RSGI
S2F
SASTAD
SECSG
SGC
SGCGES
SGPP
SPINE
SPINE-2
SSGCID
SSPF
STEMCELL
TBSGC
TCELL
TEMIMPS
TJMP
TMPC
TransportPDB
UC4CDI
XMTB
YSG
Examples
JCSG
Structural Genomics Project Center Name
Attributepdbx_SG_project.full_name_of_center
DescriptionThe value identifies the full name of center.
Typestring
Enumeration
Accelerated Technologies Center for Gene to 3D Structure
Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions
Atoms-to-Animals: The Immune Function Network
Bacterial targets at IGS-CNRS, France
Berkeley Structural Genomics Center
Center for Eukaryotic Structural Genomics
Center for High-Throughput Structural Biology
Center for Membrane Proteins of Infectious Diseases
Center for Structural Genomics of Infectious Diseases
Center for Structures of Membrane Proteins
Center for the X-ray Structure Determination of Human Transporters
Chaperone-Enabled Studies of Epigenetic Regulation Enzymes
Enzyme Discovery for Natural Product Biosynthesis
GPCR Network
Integrated Center for Structure and Function Innovation
Israel Structural Proteomics Center
Joint Center for Structural Genomics
Marseilles Structural Genomics Program @ AFMB
Medical Structural Genomics of Pathogenic Protozoa
Membrane Protein Structural Biology Consortium
Membrane Protein Structures by Solution NMR
Midwest Center for Macromolecular Research
Midwest Center for Structural Genomics
Mitochondrial Protein Partnership
Montreal-Kingston Bacterial Structural Genomics Initiative
Mycobacterium Tuberculosis Structural Proteomics Project
New York Consortium on Membrane Protein Structure
New York SGX Research Center for Structural Genomics
New York Structural GenomiX Research Consortium
New York Structural Genomics Research Consortium
Northeast Structural Genomics Consortium
Nucleocytoplasmic Transport: a Target for Cellular Control
Ontario Centre for Structural Proteomics
Oxford Protein Production Facility
Paris-Sud Yeast Structural Genomics
Partnership for Nuclear Receptor Signaling Code Biology
Partnership for Stem Cell Biology
Partnership for T-Cell Biology
Program for the Characterization of Secreted Effector Proteins
Protein Structure Factory
RIKEN Structural Genomics/Proteomics Initiative
Scottish Structural Proteomics Facility
Seattle Structural Genomics Center for Infectious Disease
South Africa Structural Targets Annotation Database
Southeast Collaboratory for Structural Genomics
Structural Genomics Consortium
Structural Genomics Consortium for Research on Gene Expression
Structural Genomics of Pathogenic Protozoa Consortium
Structural Proteomics in Europe
Structural Proteomics in Europe 2
Structure 2 Function Project
Structure, Dynamics and Activation Mechanisms of Chemokine Receptors
Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes
Structure-Function Studies of Tight Junction Membrane Proteins
Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
TB Structural Genomics Consortium
Transcontinental EM Initiative for Membrane Protein Structure
Transmembrane Protein Center
Examples
Midwest Center for Structural Genomics
Has Experimental Data
Attributercsb_accession_info.has_released_experimental_data
DescriptionA code indicating the current availibility of experimental data in the repository.
Typestring
Enumeration
N
Y
Examples
Y
N
Compatible with PDB Format
Attributepdbx_database_status.pdb_format_compatible
DescriptionA flag indicating that the entry is compatible with the PDB format. A value of 'N' indicates that the no PDB format data file is corresponding to this entry is available in the PDB archive.
Typestring
Enumeration
N
Y
Examples
Y
Funding Organization
Attributepdbx_audit_support.funding_organization
DescriptionThe name of the organization providing funding support for the entry. Funding information is optionally provided for entries after June 2016.
Typestring
Examples
National Institutes of Health
Wellcome Trust
National Institutes of Health/National Institute of General Medical Sciences
Funding Grant Number
Attributepdbx_audit_support.grant_number
DescriptionThe grant number associated with this source of support.
Typestring
Funding Country
Attributepdbx_audit_support.country
DescriptionThe country/region providing the funding support for the entry. Funding information is optionally provided for entries after June 2016.
Typestring
Content Types Available in the Repository
Attributercsb_repository_holdings_current.repository_content_types
DescriptionThe list of content types associated with this entry.
Typestring
Enumeration
2fo-fc Map
Combined NMR data (NEF)
Combined NMR data (NMR-STAR)
FASTA sequence
Map Coefficients
NMR chemical shifts
NMR restraints V1
NMR restraints V2
assembly PDB
assembly mmCIF
entry PDB
entry PDB bundle
entry PDBML
entry mmCIF
fo-fc Map
structure factors
validation data mmCIF
validation report
validation slider image
Examples
entry mmCIF
Content Types Available in a Related Resource
Attributepdbx_database_related.content_type
DescriptionThe identifying content type of the related entry.
Typestring
Enumeration
associated EM volume
associated NMR restraints
associated SAS data
associated structure factors
complete structure
derivative structure
ensemble
minimized average structure
native structure
other
other EM volume
protein target sequence and/or protocol data
re-refinement
representative structure
split
unspecified
Examples
minimized average structure
representative structure
ensemble
derivative structure
native structure
associated EM volume
other EM volume
associated NMR restraints
associated structure factors
associated SAS data
protein target sequence and/or protocol data
split
re-refinement
complete structure
unspecified
other
Related Resource Name Containing Additional Content
Attributepdbx_database_related.db_name
DescriptionThe name of the database containing the related entry.
Typestring
Examples
PDB - Protein Databank NDB - Nucleic Acid Database BMRB - BioMagResBank EMDB - Electron Microscopy Database BMCD - Biological Macromolecule Crystallization Database TargetTrack - Target Registration and Protocol Database SASBDB - Small Angle Scattering Biological Data Bank
Deposited Entry Features
Entry Polymer Types
Attributercsb_entry_info.selected_polymer_entity_types
DescriptionSelected polymer entity type categories describing the entry.
Typestring
Enumeration
Nucleic acid (only)
Oligosaccharide (only)
Other
Protein (only)
Protein/NA
Protein/Oligosaccharide
Examples
Protein (only)
Entry Polymer Composition
Attributercsb_entry_info.polymer_composition
DescriptionCategories describing the polymer entity composition for the entry.
Typestring
Enumeration
DNA
DNA/RNA
NA-hybrid
NA/oligosaccharide
RNA
heteromeric protein
homomeric protein
oligosaccharide
other
other type composition
other type pair
protein/NA
protein/NA/oligosaccharide
protein/oligosaccharide
Examples
homomeric protein
Molecular Weight per Deposited Model
Attributercsb_entry_info.molecular_weight
DescriptionThe molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry.
Typenumber
Minimum Value0.42
Maximum Value34852.58
Examples
33.43
45.53
Number of Distinct Molecular Entities
Attributercsb_entry_info.entity_count
DescriptionThe number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model.
Typeinteger
Minimum Value1
Maximum Value455
Number of Distinct Non-polymer Entities
Attributercsb_entry_info.nonpolymer_entity_count
DescriptionThe number of distinct non-polymer entities in the structure entry exclusive of solvent.
Typeinteger
Minimum Value0
Maximum Value30
Number of Distinct Protein Entities
Attributercsb_entry_info.polymer_entity_count_protein
DescriptionThe number of distinct protein polymer entities.
Typeinteger
Minimum Value0
Maximum Value145
Number of Distinct RNA Entities
Attributercsb_entry_info.polymer_entity_count_RNA
DescriptionThe number of distinct RNA polymer entities.
Typeinteger
Minimum Value0
Maximum Value36
Number of Distinct DNA Entities
Attributercsb_entry_info.polymer_entity_count_DNA
DescriptionThe number of distinct DNA polymer entities.
Typeinteger
Minimum Value0
Maximum Value455
Number of Distinct NA Hybrid Entities
Attributercsb_entry_info.polymer_entity_count_nucleic_acid_hybrid
DescriptionThe number of distinct hybrid nucleic acid polymer entities.
Typeinteger
Minimum Value0
Maximum Value3
Total Number of Polymer Instances (Chains)
Attributercsb_entry_info.deposited_polymer_entity_instance_count
DescriptionThe number of polymer instances in the deposited data set. This is the total count of polymer entity instances reported per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value1356
Total Number of Non-polymer Instances
Attributercsb_entry_info.deposited_nonpolymer_entity_instance_count
DescriptionThe number of non-polymer instances in the deposited data set. This is the total count of non-polymer entity instances reported per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value5351
Total Number of Polymer Residues per Deposited Model
Attributercsb_entry_info.deposited_polymer_monomer_count
DescriptionThe number of polymer monomers in sample entity instances in the deposited data set. This is the total count of monomers for all polymer entity instances reported per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value313236
Number of Non-Hydrogen Atoms per Deposited Model
Attributercsb_entry_info.deposited_atom_count
DescriptionThe number of heavy atom coordinates records per deposited structure model.
Typeinteger
Minimum Value28
Maximum Value2440800
Number of Hydrogen Atoms per Deposited Model
Attributercsb_entry_info.deposited_hydrogen_atom_count
DescriptionThe number of hydrogen atom coordinates records per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value680778
Number of Water Molecules per Deposited Model
Attributercsb_entry_info.deposited_solvent_atom_count
DescriptionThe number of heavy solvent atom coordinates records per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value15347
Deposited Model Count
Attributercsb_entry_info.deposited_model_count
DescriptionThe number of model structures deposited.
Typeinteger
Minimum Value1
Maximum Value640
Disulfide Bond Count per Deposited Model
Attributercsb_entry_info.disulfide_bond_count
DescriptionThe number of disulfide bonds per deposited structure model.
Typeinteger
Minimum Value0
Maximum Value1356
Polymer Molecular Features
Polymer Entity Description
Attributercsb_polymer_entity.pdbx_description
DescriptionA description of the polymer entity.
Typestring
Examples
Green fluorescent protein
23S ribosomal RNA
NAD-dependent protein deacylase sirtuin-5, mitochondrial
Macromolecule Name
Attributercsb_polymer_entity.rcsb_macromolecular_names_combined.name
DescriptionCombined list of macromolecular names.
Typestring
Examples
Lysozyme C
Plasmid recombination enzyme
Pyruvate carboxylase
Polymer Entity Type
Attributeentity_poly.rcsb_entity_polymer_type
DescriptionA coarse-grained polymer entity type.
Typestring
Enumeration
Protein
DNA
RNA
NA-hybrid
Other
Polymer Entity Sequence Length
Attributeentity_poly.rcsb_sample_sequence_length
DescriptionThe monomer length of the sample sequence.
Typeinteger
Minimum Value1
Maximum Value19000
Polymer Entity Mutation Count
Attributeentity_poly.rcsb_mutation_count
DescriptionNumber of engineered mutations engineered in the sample sequence.
Typeinteger
Minimum Value0
Maximum Value657
Polymer Entity Molecular Weight
Attributercsb_polymer_entity.formula_weight
DescriptionFormula mass (KDa) of the entity.
Typenumber
Minimum Value0.16
Maximum Value6061.92
Examples
40
105
Glycosylation Site
Attributercsb_polymer_struct_conn.role
DescriptionThe chemical or structural role of the interaction
Typestring
Enumeration
C-Mannosylation
N-Glycosylation
O-Glycosylation
S-Glycosylation
Examples
N-Glycosylation
O-Glycosylation
Gene Name
Attributercsb_entity_source_organism.rcsb_gene_name.value
DescriptionGene name.
Typestring
Examples
lacA
hemH
Source Organism Taxonomy Name (Full Lineage)
Attributercsb_entity_source_organism.taxonomy_lineage.name
DescriptionMemebers of the NCBI Taxonomy lineage as parent taxonomy names.
Typestring
Examples
Homo sapiens
Mus musculus
Polymer Entity Name Combined
Attributercsb_polymer_entity.rcsb_polymer_name_combined.names
DescriptionProtein name annotated by the UniProtKB or macromolecular name assigned by the PDB
Typestring
Source Organism Taxonomy ID (Full Lineage)
Attributercsb_entity_source_organism.taxonomy_lineage.id
DescriptionMembers of the NCBI Taxonomy lineage as parent taxonomy idcodes.
Typestring
Examples
9606
10090
Scientific Name of the Source Organism
Attributercsb_entity_source_organism.ncbi_scientific_name
DescriptionThe scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database. This name corresponds to the taxonomy identifier assigned by the PDB depositor. References: Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009). GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. Epub 2008 Oct 21.
Typestring
Parent Scientific Name (typically superkingdom or clade)
Attributercsb_entity_source_organism.ncbi_parent_scientific_name
DescriptionA parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor. For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this corresponds to the first level of any taxonomic rank below the root level. References: Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009). GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. Epub 2008 Oct 21.
Typestring
Examples
Archaea
Bacteria
Eukaryota
Adnaviria
Bicaudaviridae
Clavaviridae
Duplodnaviria
Source Organism Type
Attributercsb_entity_source_organism.source_type
DescriptionThe source type for the entity
Typestring
Enumeration
genetically engineered
natural
synthetic
Polymer Entity Source Count
Attributercsb_polymer_entity.rcsb_source_part_count
DescriptionThe number of biological sources for the polymer entity. Multiple source contributions may come from the same organism (taxonomy).
Typeinteger
Minimum Value0
Maximum Value21
Polymer Entity Distinct Taxonomy Count
Attributercsb_polymer_entity.rcsb_source_taxonomy_count
DescriptionThe number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers.
Typeinteger
Minimum Value0
Maximum Value5
Expression System Organism Taxonomy Name
Attributercsb_entity_host_organism.taxonomy_lineage.name
DescriptionMembers of the NCBI Taxonomy lineage as parent taxonomy names.
Typestring
Examples
Escherichia coli BL21(DE3)
Baculovirus
Expression System Organism Taxonomy ID
Attributercsb_entity_host_organism.taxonomy_lineage.id
DescriptionMembers of the NCBI Taxonomy lineage as parent taxonomy idcodes.
Typestring
Examples
469008
10469
Enzyme Classification Number
Attributercsb_polymer_entity.rcsb_ec_lineage.id
DescriptionMembers of the enzyme classification lineage as parent classification codes.
Typestring
Examples
2
2.7.1.153
Iterabletrue
Enzyme Classification Name
Attributercsb_polymer_entity.rcsb_ec_lineage.name
DescriptionMembers of the enzyme classification lineage as parent classification names.
Typestring
Examples
Transferases
phosphatidylinositol-4,5-bisphosphate 3-kinase
Identifier - InterPro Protein Family
Attributercsb_polymer_entity_annotation.annotation_id
DescriptionAn identifier for the annotation.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
IPR022352
IPR004825
Identifier - Pfam Protein Family
Attributercsb_polymer_entity_annotation.annotation_id
DescriptionAn identifier for the annotation.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
PF00049
PF00441
Lineage Identifier - Gene Ontology
Attributercsb_polymer_entity_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
GO:0005575
GO:0005622
Lineage Identifier - Membrane Proteins of Known 3D Structure
Attributercsb_polymer_entity_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A
Lineage Identifier - Orientations of Proteins in Membranes (OPM) Database
Attributercsb_polymer_entity_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
Transmembrane.Bitopic proteins.Bitopic proteins with NAD(P)-binding Rossmann-fold domains.Flavin containing amine oxidoreductase
Lineage Name - Gene Ontology
Attributercsb_polymer_entity_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
cellular_component
intracellular
Lineage Name - Membrane Proteins of Known 3D Structure
Attributercsb_polymer_entity_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
Monoamine Oxidase A
Lineage Name - Orientations of Proteins in Membranes (OPM) Database
Attributercsb_polymer_entity_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_entity_annotation.type
Nested Attribute Examples
Flavin containing amine oxidoreductase
Chromosomal Locus (Browser ID)
Attributercsb_genomic_lineage.id
DescriptionAutomatically assigned ID that uniquely identifies taxonomy, chromosome or gene in the Genome Location Browser.
Typestring
Examples
9606
568815441
414325
Count Per Polymer Entity - Cloning artifact, expression tag, linker
Attributercsb_polymer_entity_feature_summary.count
DescriptionThe feature count.
Typeinteger
Nested Attributercsb_polymer_entity_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value22
Nested Attribute Examples
1
10
Count Per Polymer Entity - Modified chemical component
Attributercsb_polymer_entity_feature_summary.count
DescriptionThe feature count.
Typeinteger
Nested Attributercsb_polymer_entity_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value4.1e3
Nested Attribute Examples
2
5
Coverage Fraction Per Polymer Entity - Cloning artifact, expression tag, linker
Attributercsb_polymer_entity_feature_summary.coverage
DescriptionThe fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as mutations, artifacts or modified monomers relative to the length of the entity sequence.
Typenumber
Nested Attributercsb_polymer_entity_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value0.78
Nested Attribute Examples
0.02
0.12
Coverage Fraction Per Polymer Entity - Modified chemical component
Attributercsb_polymer_entity_feature_summary.coverage
DescriptionThe fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as mutations, artifacts or modified monomers relative to the length of the entity sequence.
Typenumber
Nested Attributercsb_polymer_entity_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value1.0
Nested Attribute Examples
0.01
0.05
Polymer Instance (Chain) Features
Lineage Identifier - CATH
Attributercsb_polymer_instance_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
2.30.30.40
3.30.420.40
Lineage Identifier - SCOP
Attributercsb_polymer_instance_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
82057
53067
Lineage Identifier - SCOP2 Family/Superfamily
Attributercsb_polymer_instance_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
8093789
8084640
8084641
8093790
Lineage Identifier - ECOD
Attributercsb_polymer_instance_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
e3mbgA1
e6lu7A2
Lineage Name - CATH
Attributercsb_polymer_instance_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
SH3 Domains
ATPase, nucleotide binding domain
Lineage Name - SCOP
Attributercsb_polymer_instance_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
Prokaryotic SH3-related domain
Actin-like ATPase domain
Lineage Name - SCOP2 Family/Superfamily
Attributercsb_polymer_instance_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
Sialidases (neuraminidases)
FAD-dependent thiol oxidase
FAD-dependent thiol oxidase
Sialidases
Lineage Name - ECOD
Attributercsb_polymer_instance_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_polymer_instance_annotation.type
Nested Attribute Examples
Evr1_Alr
Peptidase_C30_C
Count Per Polymer Chain - CIS-PEPTIDE
Attributercsb_polymer_instance_feature_summary.count
DescriptionThe feature count per polymer chain.
Typeinteger
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value3.0e2
Nested Attribute Examples
1
10
Count Per Polymer Chain - HELIX_P
Attributercsb_polymer_instance_feature_summary.count
DescriptionThe feature count per polymer chain.
Typeinteger
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value3.7e2
Nested Attribute Examples
1
10
Count Per Polymer Chain - SHEET
Attributercsb_polymer_instance_feature_summary.count
DescriptionThe feature count per polymer chain.
Typeinteger
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value2.1e2
Nested Attribute Examples
1
10
Count Per Polymer Chain - RSCC_OUTLIER
Attributercsb_polymer_instance_feature_summary.count
DescriptionThe feature count per polymer chain.
Typeinteger
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value2.8e3
Nested Attribute Examples
1
10
Count Per Polymer Chain - RSRZ_OUTLIER
Attributercsb_polymer_instance_feature_summary.count
DescriptionThe feature count per polymer chain.
Typeinteger
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value3.4e3
Nested Attribute Examples
1
10
Coverage Fraction Per Polymer Chain - HELIX_P
Attributercsb_polymer_instance_feature_summary.coverage
DescriptionThe fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence.
Typenumber
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value8.1
Nested Attribute Examples
0.15
0.45
Coverage Fraction Per Polymer Chain - SHEET
Attributercsb_polymer_instance_feature_summary.coverage
DescriptionThe fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence.
Typenumber
Nested Attributercsb_polymer_instance_feature_summary.type
Nested Attribute Minimum Value0
Nested Attribute Maximum Value20
Nested Attribute Examples
0.15
0.45
Nonpolymer Molecular Features
Component Identifier - Investigated Molecule
Attributercsb_nonpolymer_entity_annotation.comp_id
DescriptionNon-polymer(ligand) chemical component identifier for the entity.
Typestring
Nested Attributercsb_nonpolymer_entity_annotation.type
Nested Attribute Examples
BEZ
PQM
Binding Affinity Value - IC50
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value0.0010
Nested Attribute Maximum Value8.0e8
Nested Attribute Examples
0.8
14
UnitsnM
Binding Affinity Value - EC50
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value0.0040
Nested Attribute Maximum Value3.0e6
Nested Attribute Examples
0.18
23000
UnitsnM
Binding Affinity Value - Kd
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value6.0e-7
Nested Attribute Maximum Value1.4e9
Nested Attribute Examples
6.5
220000
UnitsnM
Binding Affinity Value - Ka
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value0.0011
Nested Attribute Maximum Value1.0e14
Nested Attribute Examples
7.5
1700
UnitsM⁻¹
Binding Affinity Value - Ki
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value0.000011
Nested Attribute Maximum Value1.0e14
Nested Attribute Examples
4
390000
UnitsnM
Binding Affinity Value - ΔG
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value-1.1e3
Nested Attribute Maximum Value30
Nested Attribute Examples
17.2
21.4
UnitskJ/mol
Binding Affinity Value - ΔH
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value-7.8e2
Nested Attribute Maximum Value73
Nested Attribute Examples
66.9
123
UnitskJ/mol
Binding Affinity Value - -TΔS
Attributercsb_binding_affinity.value
DescriptionBinding affinity value between a ligand and its target molecule.
Typenumber
Nested Attributercsb_binding_affinity.type
Nested Attribute Minimum Value-3.1e2
Nested Attribute Maximum Value1.7e3
Nested Attribute Examples
18.1
47.2
UnitskJ/mol
Oligosaccharide/Branched Molecular Features
Branched Entity Type
Attributepdbx_entity_branch.type
DescriptionThe type of this branched oligosaccharide.
Typestring
Enumeration
oligosaccharide
Oligosaccharide Entity Description
Attributercsb_branched_entity.pdbx_description
DescriptionA description of the branched entity.
Typestring
Examples
alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
Oligosaccharide Formula Weight
Attributercsb_branched_entity.formula_weight
DescriptionFormula mass (KDa) of the branched entity.
Typenumber
Minimum Value0.27
Maximum Value10.41
Examples
0.745
1.2
Oligosaccharide Linear Descriptor - LINUCS
Attributepdbx_entity_branch_descriptor.descriptor
DescriptionThis data item contains the descriptor value for this entity.
Typestring
Nested Attributepdbx_entity_branch_descriptor.type
Nested Attribute Examples
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}
Oligosaccharide Linear Descriptor - Glycam Condensed Sequence
Attributepdbx_entity_branch_descriptor.descriptor
DescriptionThis data item contains the descriptor value for this entity.
Typestring
Nested Attributepdbx_entity_branch_descriptor.type
Nested Attribute Examples
DManpa1-2DManpa1-ROH
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-
Oligosaccharide Linear Descriptor - WURCS
Attributepdbx_entity_branch_descriptor.descriptor
DescriptionThis data item contains the descriptor value for this entity.
Typestring
Nested Attributepdbx_entity_branch_descriptor.type
Nested Attribute Examples
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1
Oligosaccharide Component Count
Attributepdbx_entity_branch.rcsb_branched_component_count
DescriptionNumber of constituent chemical components in the branched entity.
Typeinteger
Minimum Value2
Maximum Value36
Oligosaccharide Component List
Attributercsb_branched_entity_container_identifiers.chem_comp_monomers
DescriptionUnique list of monomer chemical component identifiers in the entity in this container.
Typestring
Examples
NAG
MAN
GAL
Iterabletrue
Assembly Features
Number of Non-Hydrogen Atoms per Assembly
Attributercsb_assembly_info.atom_count
DescriptionThe assembly non-hydrogen atomic coordinate count.
Typeinteger
Minimum Value7
Maximum Value39959280
Number of Hydrogen Atoms per Assembly
Attributercsb_assembly_info.hydrogen_atom_count
DescriptionThe assembly hydrogen atomic coordinate count.
Typeinteger
Minimum Value0
Maximum Value5795340
Number of Water Molecules per Assembly
Attributercsb_assembly_info.solvent_atom_count
DescriptionThe assembly non-hydrogen solvent atomic coordinate count.
Typeinteger
Minimum Value0
Maximum Value78540
Number of Polymer Residues per Assembly
Attributercsb_assembly_info.polymer_monomer_count
DescriptionThe number of polymer monomers in sample entity instances comprising the assembly data set. This is the total count of monomers for all polymer entity instances in the generated assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value5340600
Number of Modeled Polymer Residues per Assembly
Attributercsb_assembly_info.modeled_polymer_monomer_count
DescriptionThe number of modeled polymer monomers in the assembly coordinate data. This is the total count of monomers with reported coordinate data for all polymer entity instances in the generated assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value5086680
Number of Unmodeled Polymer Residues per Assembly
Attributercsb_assembly_info.unmodeled_polymer_monomer_count
DescriptionThe number of unmodeled polymer monomers in the assembly coordinate data. This is the total count of monomers with unreported coordinate data for all polymer entity instances in the generated assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value515880
Number of Polymer Instances (Chains) per Assembly
Attributercsb_assembly_info.polymer_entity_instance_count
DescriptionThe number of polymer instances in the generated assembly data set. This is the total count of polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value8280
Number of Non-polymer Instances per Assembly
Attributercsb_assembly_info.nonpolymer_entity_instance_count
DescriptionThe number of non-polymer instances in the generated assembly data set exclusive of solvent. This is the total count of non-polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value3259
Number of Protein Instances (Chains) per Assembly
Attributercsb_assembly_info.polymer_entity_instance_count_protein
DescriptionThe number of protein polymer instances in the generated assembly data set. This is the total count of protein polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value8280
Number of DNA Instances (Chains) per Assembly
Attributercsb_assembly_info.polymer_entity_instance_count_DNA
DescriptionThe number of DNA polymer instances in the generated assembly data set. This is the total count of DNA polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value455
Number of RNA Instances (Chains) per Assembly
Attributercsb_assembly_info.polymer_entity_instance_count_RNA
DescriptionThe number of RNA polymer instances in the generated assembly data set. This is the total count of RNA polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value180
Number of NA Hybrid Instances (Chains) per Assembly
Attributercsb_assembly_info.polymer_entity_instance_count_nucleic_acid_hybrid
DescriptionThe number of hybrid nucleic acide polymer instances in the generated assembly data set. This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data.
Typeinteger
Minimum Value0
Maximum Value8
Assembly Experimental Support
Attributepdbx_struct_assembly_auth_evidence.experimental_support
DescriptionProvides the experimental method to determine the state of this assembly
Typestring
Enumeration
NMR Distance Restraints
NMR relaxation study
SAXS
assay for oligomerization
cross-linking
electron microscopy
equilibrium centrifugation
fluorescence resonance energy transfer
gel filtration
homology
immunoprecipitation
isothermal titration calorimetry
light scattering
mass spectrometry
microscopy
native gel electrophoresis
none
scanning transmission electron microscopy
surface plasmon resonance
Assembly Experimental Support Details
Attributepdbx_struct_assembly_auth_evidence.details
DescriptionProvides any additional information regarding the evidence of this assembly
Typestring
Examples
Homology to bacteriorhodopsin
Helical filament was observed by negative staining and Cryo-EM
Symmetry Symbol
Attributercsb_struct_symmetry.symbol
DescriptionSymmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schönflies notation. Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.
Typestring
Examples
C1
D3
H
Oligomeric State
Attributercsb_struct_symmetry.oligomeric_state
DescriptionOligomeric state refers to a composition of polymeric subunits in quaternary structure. Quaternary structure may be composed either exclusively of several copies of identical subunits, in which case they are termed homo-oligomers, or alternatively by at least one copy of different subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'.
Typestring
Examples
Monomer
Homo 2-mer
Hetero 3-mer
Symmetry Type
Attributercsb_struct_symmetry.type
DescriptionSymmetry type refers to point group or helical symmetry of identical polymeric subunits. Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry.
Typestring
Enumeration
Asymmetric
Cyclic
Dihedral
Helical
Icosahedral
Octahedral
Tetrahedral
Symmetry Class
Attributercsb_struct_symmetry.kind
DescriptionThe granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered. In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed.
Typestring
Enumeration
Global Symmetry
Local Symmetry
Pseudo Symmetry
Protein Symmetry (Browser ID)
Attributercsb_struct_symmetry_lineage.id
DescriptionAutomatically assigned ID to uniquely identify the symmetry term in the Protein Symmetry Browser.
Typestring
Examples
Global Symmetry.Cyclic.C2.Homo 2-mer
Methods
Experimental Method
Attributeexptl.method
DescriptionThe method used in the experiment.
Typestring
Enumeration
X-RAY DIFFRACTION
ELECTRON MICROSCOPY
SOLID-STATE NMR
SOLUTION NMR
NEUTRON DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
POWDER DIFFRACTION
FIBER DIFFRACTION
SOLUTION SCATTERING
EPR
FLUORESCENCE TRANSFER
INFRARED SPECTROSCOPY
THEORETICAL MODEL
Examples
X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING
POWDER DIFFRACTION
Experimental Method (Broader Categories)
Attributercsb_entry_info.experimental_method
DescriptionThe category of experimental method(s) used to determine the structure entry.
Typestring
Enumeration
EM
Multiple methods
NMR
Neutron
Other
X-ray
Examples
X-ray
Number of Experimental Methods
Attributercsb_entry_info.experimental_method_count
DescriptionThe number of experimental methods contributing data to the structure determination.
Typeinteger
Minimum Value1
Maximum Value3
Refinement Resolution
Attributercsb_entry_info.resolution_combined
DescriptionCombined estimates of experimental resolution contributing to the refined structural model.
Typenumber
Minimum Value0.48
Maximum Value70
Examples
1.11
2.05
Software
Attributercsb_entry_info.software_programs_combined
DescriptionCombined list of software programs names reported in connection with the production of this entry.
Typestring
Examples
PHASER
PHENIX
REFMAC
X-ray Method Details
Structure Determination Method
Attributerefine.pdbx_method_to_determine_struct
DescriptionMethod(s) used to determine the structure.
Typestring
Examples
AB INITIO PHASING
DM
ISAS
ISIR
ISIRAS
MAD
MIR
MIRAS
MR
SIR
SIRAS
Average B Factor
Attributerefine.B_iso_mean
DescriptionThe mean isotropic displacement parameter (B value) for the coordinate set.
Typenumber
Minimum Value-13.76
Maximum Value696.1
Refinement R Factors (Observed)
Attributerefine.ls_R_factor_obs
DescriptionResidual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
Typenumber
Minimum Value0.04
Maximum Value0.98
Refinement R Factors (All)
Attributerefine.ls_R_factor_all
DescriptionResidual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
Typenumber
Minimum Value0
Maximum Value1
Refinement R Factors (R Work)
Attributerefine.ls_R_factor_R_work
DescriptionResidual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
Typenumber
Minimum Value0.04
Maximum Value0.61
Refinement R Factors (R Free)
Attributerefine.ls_R_factor_R_free
DescriptionResidual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
Typenumber
Minimum Value0.05
Maximum Value0.56
Structure Refinement Details
Attributerefine.details
DescriptionDescription of special aspects of the refinement process.
Typestring
Examples
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
X-ray Data Collection Details
Data Collection Resolution
Attributercsb_entry_info.diffrn_resolution_high.value
DescriptionThe high resolution limit of data collection.
Typenumber
Minimum Value0.29
Maximum Value15
B Wilson Estimate
Attributereflns.B_iso_Wilson_estimate
DescriptionThe value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot.
Typenumber
Minimum Value-16.8
Maximum Value926.75
Overall Redundancy
Attributereflns.pdbx_redundancy
DescriptionOverall redundancy for this data set.
Typenumber
Minimum Value-9999
Maximum Value26558
Percentage of Possible Reflections
Attributereflns.percent_possible_obs
DescriptionThe percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion.
Typenumber
Minimum Value0.04
Maximum Value100
R Value for Merging Intensities (Observed)
Attributereflns.pdbx_Rmerge_I_obs
DescriptionThe R value for merging intensities satisfying the observed criteria in this data set.
Typenumber
Minimum Value0
Maximum Value9.9
Diffraction Detector
Attributediffrn_detector.type
DescriptionThe make, model or name of the detector device used.
Typestring
Examples
DECTRIS PILATUS 12M
RAYONIX MX-325
Diffraction Source Synchrotron Site
Attributediffrn_source.pdbx_synchrotron_site
DescriptionSynchrotron site.
Typestring
Examples
APS
NSLS-II
Diffraction Source Synchrotron Beamline
Attributediffrn_source.pdbx_synchrotron_beamline
DescriptionSynchrotron beamline.
Typestring
Examples
17-ID-1
19-ID
Diffraction Source General Class
Attributediffrn_source.source
DescriptionThe general class of the radiation source.
Typestring
Examples
sealed X-ray tube
nuclear reactor
spallation source
electron microscope
rotating-anode X-ray tube
synchrotron
Diffraction Source Temperature
Attributediffrn.ambient_temp
DescriptionThe mean temperature in kelvins at which the intensities were measured.
Typenumber
Minimum Value4
Maximum Value446.15
Minimum Diffraction Wavelength
Attributercsb_entry_info.diffrn_radiation_wavelength_minimum
DescriptionThe minimum radiation wavelength in angstroms.
Typenumber
Minimum Value0
Maximum Value6.2
Maximum Diffraction Wavelength
Attributercsb_entry_info.diffrn_radiation_wavelength_maximum
DescriptionThe maximum radiation wavelength in angstroms.
Typenumber
Minimum Value0
Maximum Value15406
Cell Dimensions and Space Group
Length a
Attributecell.length_a
DescriptionUnit-cell length a corresponding to the structure reported in angstroms.
Typenumber
Minimum Value1
Maximum Value1255
Length b
Attributecell.length_b
DescriptionUnit-cell length b corresponding to the structure reported in angstroms.
Typenumber
Minimum Value1
Maximum Value1255
Length c
Attributecell.length_c
DescriptionUnit-cell length c corresponding to the structure reported in angstroms.
Typenumber
Minimum Value1
Maximum Value1933.3
Angle alpha
Attributecell.angle_alpha
DescriptionUnit-cell angle alpha of the reported structure in degrees.
Typenumber
Minimum Value58.8
Maximum Value124.81
Angle beta
Attributecell.angle_beta
DescriptionUnit-cell angle beta of the reported structure in degrees.
Typenumber
Minimum Value45.4
Maximum Value149.9
Angle gamma
Attributecell.angle_gamma
DescriptionUnit-cell angle gamma of the reported structure in degrees.
Typenumber
Minimum Value57.76
Maximum Value125
Space Group
Attributesymmetry.space_group_name_H_M
DescriptionHermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes.
Typestring
Examples
A 1
A 1 2 1
A 2
B 1 1 2
B 2
B 2 21 2
C 2
C 1 2 1
C 21
C 1 21 1
C 2(A 112)
C 2 2 2
C 2 2 21
C 4 21 2
F 2 2 2
F 2 3
F 4 2 2
F 4 3 2
F 41 3 2
I 1 2 1
I 1 21 1
I 2
I 2 2 2
I 2 3
I 21
I 21 3
I 21 21 21
I 4
I 4 2 2
I 4 3 2
I 41
I 41/a
I 41 2 2
I 41 3 2
P 1
P 1-
P 2
P 1 2 1
P 1 1 2
P 2 2 2
P 2 3
P 2 2 21
P 2 21 21
P 21
P 1 21 1
P 1 21/c 1
P 1 1 21
P 21(C)
P 21 2 21
P 21 3
P 21 21 2
P 21 21 2 A
P 21 21 21
P 3
P 3 1 2
P 3 2 1
P 31
P 31 1 2
P 31 2 1
P 32
P 32 1 2
P 32 2 1
P 4
P 4 2 2
P 4 3 2
P 4 21 2
P 41
P 41 2 2
P 41 3 2
P 41 21 2
P 42
P 42 2 2
P 42 3 2
P 42 21 2
P 43
P 43 2 2
P 43 3 2
P 43 21 2
P 6
P 6 2 2
P 61
P 61 2 2
P 62
P 62 2 2
P 63
P 63 2 2
P 64
P 64 2 2
P 65
P 65 2 2
H 3
R 3
H 3 2
R 3 2
Crystal Properties
Density (Matthews)
Attributeexptl_crystal.density_Matthews
DescriptionThe density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
Typenumber
Minimum Value0
Maximum Value13.89
Examples
3.1
Density (% solvent)
Attributeexptl_crystal.density_percent_sol
DescriptionDensity value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule
Typenumber
Minimum Value0
Maximum Value92
Temperature
Attributeexptl_crystal_grow.temp
DescriptionThe temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details.
Typenumber
Minimum Value100
Maximum Value328
pH
Attributeexptl_crystal_grow.pH
DescriptionThe pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details.
Typenumber
Minimum Value0
Maximum Value12
Examples
7.4
7.6
4.3
Crystallization Method
Attributeexptl_crystal_grow.method
DescriptionThe method used to grow the crystals.
Typestring
Examples
MICROBATCH
VAPOR DIFFUSION, HANGING DROP
Crystallization Details
Attributeexptl_crystal_grow.pdbx_details
DescriptionText description of crystal growth procedure.
Typestring
Examples
PEG 4000, potassium phosphate, magnesium chloride, cacodylate
EM Method Details
Reconstruction Resolution
Attributeem_3d_reconstruction.resolution
DescriptionThe final resolution (in Angstroms)of the 3D reconstruction.
Typenumber
Minimum Value0.6
Maximum Value70
Examples
8.9
10
EM Specimen Aggregation State
Attributeem_experiment.aggregation_state
DescriptionThe aggregation/assembly state of the imaged specimen.
Typestring
Enumeration
PARTICLE
CELL
FILAMENT
HELICAL ARRAY
2D ARRAY
3D ARRAY
TISSUE
EM Reconstruction Method
Attributeem_experiment.reconstruction_method
DescriptionThe reconstruction method used in the EM experiment.
Typestring
Enumeration
CRYSTALLOGRAPHY
HELICAL
SINGLE PARTICLE
SUBTOMOGRAM AVERAGING
TOMOGRAPHY
EM Reconstruction Software
Attributeem_software.name
DescriptionThe name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field.
Typestring
Examples
EMAN
Imagic
Spider
Bsoft
UCSF-Chimera
EM Vitrification Instrument
Attributeem_vitrification.instrument
DescriptionThe type of instrument used in the vitrification process.
Typestring
Enumeration
EMS-002 RAPID IMMERSION FREEZER
FEI VITROBOT MARK I
FEI VITROBOT MARK II
FEI VITROBOT MARK III
FEI VITROBOT MARK IV
GATAN CRYOPLUNGE 3
HOMEMADE PLUNGER
LEICA EM CPC
LEICA EM GP
LEICA KF80
LEICA PLUNGER
REICHERT-JUNG PLUNGER
SPOTITON
ZEISS PLUNGE FREEZER CRYOBOX
EM Microscope Model
Attributeem_imaging.microscope_model
DescriptionThe name of the model of microscope.
Typestring
Enumeration
FEI MORGAGNI
FEI POLARA 300
FEI TALOS ARCTICA
FEI TECNAI 10
FEI TECNAI 12
FEI TECNAI 20
FEI TECNAI ARCTICA
FEI TECNAI F20
FEI TECNAI F30
FEI TECNAI SPHERA
FEI TECNAI SPIRIT
FEI TITAN
FEI TITAN KRIOS
FEI/PHILIPS CM10
FEI/PHILIPS CM12
FEI/PHILIPS CM120T
FEI/PHILIPS CM200FEG
FEI/PHILIPS CM200FEG/SOPHIE
FEI/PHILIPS CM200FEG/ST
FEI/PHILIPS CM200FEG/UT
FEI/PHILIPS CM200T
FEI/PHILIPS CM300FEG/HE
FEI/PHILIPS CM300FEG/ST
FEI/PHILIPS CM300FEG/T
FEI/PHILIPS EM400
FEI/PHILIPS EM420
HITACHI EF2000
HITACHI EF3000
HITACHI H-9500SD
HITACHI H3000 UHVEM
HITACHI H7600
HITACHI HF2000
HITACHI HF3000
JEOL 1000EES
JEOL 100B
JEOL 100CX
JEOL 1010
JEOL 1200
JEOL 1200EX
JEOL 1200EXII
JEOL 1230
JEOL 1400
JEOL 2000EX
JEOL 2000EXII
JEOL 2010
JEOL 2010F
JEOL 2010HC
JEOL 2010HT
JEOL 2010UHR
JEOL 2011
JEOL 2100
JEOL 2100F
JEOL 2200FS
JEOL 2200FSC
JEOL 3000SFF
JEOL 3100FEF
JEOL 3100FFC
JEOL 3200FS
JEOL 3200FSC
JEOL 4000
JEOL 4000EX
JEOL CRYO ARM 200
JEOL CRYO ARM 300
JEOL KYOTO-3000SFF
SIEMENS SULEIKA
TFS GLACIOS
TFS KRIOS
TFS TALOS
TFS TALOS F200C
TFS TALOS L120C
TFS TUNDRA
ZEISS LEO912
ZEISS LIBRA120PLUS
EM Accelerating Voltage
Attributeem_imaging.accelerating_voltage
DescriptionA value of accelerating voltage (in kV) used for imaging.
Typeinteger
Minimum Value45
Maximum Value400
EM Imaging Detector
Attributeem_image_recording.film_or_detector_model
DescriptionThe detector type used for recording images. Usually film or CCD camera.
Typestring
EM Point Symmetry Imposed
Attributeem_single_particle_entity.point_symmetry
DescriptionPoint symmetry symbol, either Cn, Dn, T, O, or I
Typestring
Examples
C1
C5
C4
EM Staining Material
Attributeem_staining.material
DescriptionThe staining material.
Typestring
Examples
Uranyl Acetate
NMR Method Details
NMR Spectrometer Manufacturer
Attributepdbx_nmr_spectrometer.manufacturer
DescriptionThe name of the manufacturer of the spectrometer.
Typestring
Examples
Varian
Bruker
JEOL
GE
NMR Spectrometer Model
Attributepdbx_nmr_spectrometer.model
DescriptionThe model of the NMR spectrometer.
Typestring
Examples
AVANCE
AVANCE II
AVANCE III
AVANCE III HD
WH
WM
AM
AMX
DMX
DRX
MSL
OMEGA
OMEGA PSG
GX
GSX
A
AL
EC
EX
LA
ECP
VXRS
UNITY
UNITYPLUS
INOVA
NMR Spectrometer Field Strength
Attributepdbx_nmr_spectrometer.field_strength
DescriptionThe field strength in MHz of the spectrometer
Typenumber
Minimum Value0
Maximum Value3400
NMR Method to Determination Structure
Attributepdbx_nmr_refine.method
DescriptionThe method used to determine the structure.
Typestring
Examples
simulated annealing
distance geometry simulated annealing molecular dynamics matrix relaxation torsion angle dynamics
Linked External Resources
Experimental Data Resource
Attributercsb_external_references.type
DescriptionInternal identifier for external resource.
Typestring
Enumeration
BMRB
EM DATA RESOURCE
NDB
OLDERADO
PROTEIN DIFFRACTION
SB GRID
UniProt-mapped Resource
Attributercsb_uniprot_external_reference.reference_name
Description
Typestring
Enumeration
GTEX
IMPC
PHAROS
Publications Primary
Primary Citation Author
Attributercsb_primary_citation.rcsb_authors
DescriptionNames of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Typestring
Examples
Bleary, Percival R.
Primary Citation Title
Attributercsb_primary_citation.title
DescriptionThe title of the citation; relevant for journal articles, books and book chapters.
Typestring
Examples
Structure of diferric duck ovotransferrin at 2.35 Angstroms resolution.
Primary Citation Journal Name (Abbreviated)
Attributercsb_primary_citation.rcsb_journal_abbrev
DescriptionNormalized journal abbreviation.
Typestring
Examples
Nat Struct Mol Biol
Primary Citation Publication Year
Attributercsb_primary_citation.year
DescriptionThe year of the citation; relevant for journal articles, books and book chapters.
Typeinteger
Minimum Value1969
Maximum Value2022
Primary Citation DOI
Attributercsb_primary_citation.pdbx_database_id_DOI
DescriptionDocument Object Identifier used by doi.org to uniquely specify bibliographic entry.
Typestring
Examples
10.2345/S1384107697000225
Primary Citation Author ORCID
Attributercsb_primary_citation.rcsb_ORCID_identifiers
DescriptionThe Open Researcher and Contributor ID (ORCID) identifiers for the citation authors.
Typestring
Examples
0000-0002-6681-547X
PubMed Abstract
Attributercsb_pubmed_abstract_text
DescriptionA concise, accurate and factual mini-version of the paper contents.
Typestring
MeSH Identifier
Attributercsb_pubmed_mesh_descriptors_lineage.id
DescriptionIdentifier for MeSH classification term.
Typestring
Examples
E01.370.225.500.388
H01.181
MeSH Descriptor
Attributercsb_pubmed_mesh_descriptors_lineage.name
DescriptionMeSH classification term.
Typestring
Examples
Chemistry
Mammals
Therapeutic Uses
Publications All
Citation Author
Attributecitation.rcsb_authors
DescriptionNames of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Typestring
Examples
Bleary, Percival R.
Citation Title
Attributecitation.title
DescriptionThe title of the citation; relevant for journal articles, books and book chapters.
Typestring
Examples
Structure of diferric duck ovotransferrin at 2.35 Angstroms resolution.
Citation Journal Name (Abbreviated)
Attributecitation.rcsb_journal_abbrev
DescriptionNormalized journal abbreviation.
Typestring
Examples
Nat Struct Mol Biol
Citation Publication Year
Attributecitation.year
DescriptionThe year of the citation; relevant for journal articles, books and book chapters.
Typeinteger
Minimum Value1947
Maximum Value2022
Citation DOI
Attributecitation.pdbx_database_id_DOI
DescriptionDocument Object Identifier used by doi.org to uniquely specify bibliographic entry.
Typestring
Examples
10.2345/S1384107697000225

Chemical Attributes

Chemical Components
Chemical ID(s)
Attributercsb_chem_comp_container_identifiers.comp_id
DescriptionThe chemical component identifier.
Typestring
Examples
ATP
STI
Iterabletrue
Chemical Name
Attributechem_comp.name
DescriptionThe full name of the component.
Typestring
Examples
alanine
valine
adenine
cytosine
Chemical Synonyms
Attributercsb_chem_comp_synonyms.name
DescriptionThe synonym of this particular chemical component.
Typestring
Examples
Ursonic acid
Talotrexin
4-oxodecanedioic acid
Chemical Component Release Date
Attributercsb_chem_comp_info.initial_release_date
DescriptionThe initial date the chemical definition was released in the PDB repository.
Typestring
Minimum Value5/2/1973
Maximum Value5/17/2022
Examples
2016-09-11
Chemical Component Type
Attributechem_comp.type
DescriptionFor standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap.
Typestring
Enumeration
D-beta-peptide, C-gamma linking
D-gamma-peptide, C-delta linking
D-peptide COOH carboxy terminus
D-peptide NH3 amino terminus
D-peptide linking
D-saccharide
D-saccharide, alpha linking
D-saccharide, beta linking
DNA OH 3 prime terminus
DNA OH 5 prime terminus
DNA linking
L-DNA linking
L-RNA linking
L-beta-peptide, C-gamma linking
L-gamma-peptide, C-delta linking
L-peptide COOH carboxy terminus
L-peptide NH3 amino terminus
L-peptide linking
L-saccharide
L-saccharide, alpha linking
L-saccharide, beta linking
RNA OH 3 prime terminus
RNA OH 5 prime terminus
RNA linking
non-polymer
other
peptide linking
peptide-like
saccharide
Drug Target Name
Attributercsb_chem_comp_target.name
DescriptionThe chemical component target name.
Typestring
InChiKey
Attributercsb_chem_comp_descriptor.InChIKey
DescriptionStandard IUPAC International Chemical Identifier (InChI) descriptor key for the chemical component InChI, the IUPAC International Chemical Identifier, by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi, Journal of Cheminformatics, 2015, 7:23
Typestring
Examples
BNOCDEBUFVJMQI-REOHCLBHSA-N
Chemical Component Molecular Weight
Attributechem_comp.formula_weight
DescriptionFormula mass of the chemical component.
Typenumber
Minimum Value2.01
Maximum Value5496.51
Examples
120.12
450.1
Chemical Component Nonhydrogen Atom Count
Attributercsb_chem_comp_info.atom_count_heavy
DescriptionChemical component heavy atom count
Typeinteger
Minimum Value0
Maximum Value352
Chemical Component Chiral Atom Count
Attributercsb_chem_comp_info.atom_count_chiral
DescriptionChemical component chiral atom count
Typeinteger
Minimum Value0
Maximum Value48
Chemical Component Bond Count
Attributercsb_chem_comp_info.bond_count
DescriptionChemical component total bond count
Typeinteger
Minimum Value0
Maximum Value727
Chemical Component Aromatic Bond Count
Attributercsb_chem_comp_info.bond_count_aromatic
DescriptionChemical component aromatic bond count
Typeinteger
Minimum Value0
Maximum Value97
Identifier Codes - DrugBank
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
DB06830
DB07255
Identifier Codes - CCDC/CSD
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
QAXDEZ
XEGJEA
Identifier Codes - RESID
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
AA0078
AA0034
Identifier Codes - PubChem
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
3082729
5289380
Identifier Codes - ChEBI
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
CHEBI:151557
CHEBI:6198
Identifier Codes - ChEMBL
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
CHEMBL1165239
CHEMBL3330255
Identifier Codes - CAS Registry Number
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
2133-34-8
30565-25-4
Identifier Codes - Pharos
Attributercsb_chem_comp_related.resource_accession_code
DescriptionThe resource identifier code for the related chemical reference.
Typestring
Nested Attributercsb_chem_comp_related.resource_name
Nested Attribute Examples
CHEMBL1165239
CHEMBL3330255
Name - RESID Generating Enzyme
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
protein N-terminal methyltransferase (EC 2.1.1.-)
autocatalytic
Name - RESID Modification
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
Thyroxine
N4-methylasparagine
Name - Carbohydrate Anomer
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
alpha
beta
Name - Carbohydrate Isomer
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
D
L
Name - Carbohydrate Ring
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
pyranose
furanose
Name - Carbohydrate Primary Carbonyl Group
Attributercsb_chem_comp_annotation.name
DescriptionA name for the annotation.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
aldose
ketose
Lineage Name - ATC (WHO)
Attributercsb_chem_comp_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
lisuride
etacrynic acid
Lineage Name - PSI-MOD
Attributercsb_chem_comp_annotation.annotation_lineage.name
DescriptionMembers of the annotation lineage as parent class names.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
monomethylated residue
alpha-amino monomethylated residue
Lineage Identifier - ATC (WHO)
Attributercsb_chem_comp_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
G02CB02
C03CC01
Lineage Identifier - PSI-MOD
Attributercsb_chem_comp_annotation.annotation_lineage.id
DescriptionMembers of the annotation lineage as parent class identifiers.
Typestring
Nested Attributercsb_chem_comp_annotation.type
Nested Attribute Examples
MOD:00599
MOD:01680
Biologically Interesting Molecules (BIRD)
BIRD ID(s)
Attributepdbx_reference_molecule.prd_id
DescriptionThe value of _pdbx_reference_molecule.prd_id is the unique identifier for the reference molecule in this family. By convention this ID uniquely identifies the reference molecule in in the PDB reference dictionary. The ID has the template form PRD_dddddd (e.g. PRD_000001)
Typestring
Examples
PRD_000001
PRD_0000010
Iterabletrue
BIRD Name
Attributepdbx_reference_molecule.name
DescriptionA name of the entity.
Typestring
Examples
thiostrepton
BIRD Type
Attributepdbx_reference_molecule.type
DescriptionDefines the structural classification of the entity.
Typestring
Enumeration
Amino acid
Aminoglycoside
Ansamycin
Anthracycline
Anthraquinone
Chalkophore
Chalkophore, Polypeptide
Chromophore
Cyclic depsipeptide
Cyclic lipopeptide
Cyclic peptide
Glycopeptide
Heterocyclic
Imino sugar
Keto acid
Lipoglycopeptide
Lipopeptide
Macrolide
Non-polymer
Nucleoside
Oligopeptide
Oligosaccharide
Peptaibol
Peptide-like
Polycyclic
Polypeptide
Polysaccharide
Quinolone
Siderophore
Thiolactone
Thiopeptide
Unknown
Examples
Peptide-like
Macrolide
BIRD Class
Attributepdbx_reference_molecule.class
DescriptionBroadly defines the function of the entity.
Typestring
Enumeration
Antagonist
Anthelmintic
Antibiotic
Antibiotic, Anthelmintic
Antibiotic, Antimicrobial
Antibiotic, Antineoplastic
Anticancer
Anticoagulant
Anticoagulant, Antithrombotic
Antifungal
Antigen
Antiinflammatory
Antimicrobial
Antimicrobial, Antiparasitic, Antibiotic
Antimicrobial, Antiretroviral
Antimicrobial, Antitumor
Antineoplastic
Antiparasitic
Antiretroviral
Antithrombotic
Antitumor
Antiviral
CASPASE inhibitor
Chaperone binding
Drug delivery
Enzyme inhibitor
Glycan component
Growth factor
Immunosuppressant
Inducer
Inhibitor
Lantibiotic
Metabolism
Metal transport
Nutrient
Oxidation-reduction
Protein binding
Receptor
Substrate analog
Synthetic opioid
Thrombin inhibitor
Thrombin inhibitor, Trypsin inhibitor
Toxin
Transition state mimetic
Transport activator
Trypsin inhibitor
Unknown
Water retention


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Last updated: Tue May 17 2022