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September Molecule of the Month
DNA-Sequencing Nanopores
Deposition Preparation Tools
Data Extraction
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Small Molecules
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Validation Services
Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. These reports are developed using the recommendations of thewwPDB Validation Task Forces.
Reports for released entries are available from Structure Summary pages.
Validation reports for manuscript reviewers are created during annotation of deposited structures.
Have non-atomic coordinates, multi-scale structures obtained through integrative/hybrid (I/H) methods? Deposit at PDB-Dev which is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods.
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The Advanced Search Query Builder tool allows you to construct complex boolean queries by specifying values for a wide range of structure attributes.
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Search protein and nucleic acid sequences using the mmseqs2 method to find similar protein or nucleic acid chains in the PDB.
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Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase
Provides a graphical summary of biological and structural protein features of PDB entities and how they correspond to UniProtKB sequences. It loads features from RCSB PDB webservices and third party resources such as UniProtKB, CATH or SCOPe.
This feature is available in Structure Summary pages and Instance Sequence pages.
Genome View
Illustrates the correspondences between PDB Entity sequences and genomes.
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This feature is available from the Structure Summary page Genome tab.
Pairwise Structure Alignment
The protein structure alignment tool allows for calculating pairwise structure alignments using different alignment methods.
See the detailed documentation at this help page. Comparisons can be made for
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Also, the standalone Mol* viewer application allows for calculating pairwise structure alignments based on sequence alignment. See
detailed instructions on how to superpose structures at the Mol* help page.
Protein Symmetry
The Mol* symmetry display mode (select the Assembly Symmetry button) highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.
Structure Summary pages provide access to information about structure quality.
The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks (black vertical boxes) are calculated with respect to all X-ray structures available prior to 2011. Resolution-specific percentile ranks (white vertical boxes) are calculated considering entries with similar resolution.
This graphic is from the wwPDBValidation Report , which provides a more detailed assessment of the quality of a structure and highlights specific concerns. These reports were created using the recommendations of wwPDB Validation Task Forces.The full wwPDB Validation Report PDF is available for download. PDFs of Ramachandran plots (created by MolProbity) are provided to offer an independent method to evaluate the conformational quality of protein structures.
For examples, view the Structure Summary pages for 1CBS (1.8Å structure of a small protein and a ligand , an entry with better overall quality relative to all X-ray structures) and 1FCC (a 3.2Å structure with worse overall quality relative to all X-ray structures).
Map Genomic Locations to/from PDB
The 1D-coordinates API provides means to map between genomic coordinates and PDB positions. Find more information about this and other APIs in the webservices page.
EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.
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Experimental Data Files can be downloaded in the following formats:
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Journals, PDB users, and software developers should review code and begin to prepare for the change in format of PDB IDs and inclusion of PDB DOIs in PDBx/mmCIF files
Congratulations to Karthik Srinivasan for Structural analysis of the Toc75 Potra domains from Pisum sativum and an honorable mention to Brenna Norton-Baker for A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip » 08/24/2021
A symposium on Understanding Enzyme Function in 3D: Celebrating 50 Years of the Protein Data Bank will be held as part of the American Chemical Society Fall 2021 meeting » 08/17/2021
Download the 2020 Annual Report (PDF) for an overview of activities relating to Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education.
