File Download Services

The PDB archive

Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at the main archive, ftp.wwpdb.org (data download details) and the versioned archive, ftp-versioned.wwpdb.org (versioning details).

Protocols: FTP and HTTPS

All data are available via FTP and HTTPS. FTP users should switch to binary mode before downloading data files. Some web browsers (e.g., Chrome) have dropped support for FTP.

The HTTPS protocol offers more flexibility and less overhead and is strongly recommended for usage in scripts and third party software. HTTPS links for this service are described below. RCSB PDB additionally hosts the archive as part of the Registry of Open Data on Amazon Web Services (AWS) at https://s3.rcsb.org following the FTP directory structure.

Automated download of data

The URLs in this document are useful for scripted downloads using utilities such as wget. For instance you can consider using the batch downloads shell script.

The RCSB PDB also provides rsync capabilities, useful when maintaining full copies of the archive. These are 2 example scripts to assist in the automated download of data with rsync:

Additional information on obtaining and maintaining copies of the entire PDB archive or certain portions of it is available at https://www.wwpdb.org/downloads.html.

Major directories in the PDB archive

The directory pub/pdb is the entry directory for the ftp site.

Some general notes:

  • Entry files are date-stamped to show the date they were released
  • Entries are grouped by the middle two characters of the 4-character PDB identifier. For example, entry file pdb100d.ent can be found in pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz
  • The two letter naming convention for structure holdings is retained for the directories within /pub/pdb/data/structures/divided and /pub/pdb/data/structures/divided/obsolete but not for the directories within /pub/pdb/data/structures/all, which contain the structure holdings in undivided layout.
  • PDB entries are available in PDB, mmCIF, and PDBML/XML format.
  • Only UNIX compressed files are supported for coordinates, structure factors, and restraints.

For information about large structures that cannot be represented in the legacy PDB file format see here.

/pub/pdb/data/assemblies/mmCIFBiological assembly coordinate files in mmCIF format
/pub/pdb/data/biounit/PDBBiological assembly coordinate files in PDB format
/pub/pdb/data/monomersPDB Chemical Component Dictionary and other info on monomers
/pub/pdb/data/statusDetails of entries on hold and in processing
/pub/pdb/data/structures/allAnalogous to the divided directory, containing pdb, mmCIF, nmr_restraint, and structure_factors directories, with symbolic links to files in the divided subdirectories. In the ./all directory, files are not divided into two-letter directories, however.
/pub/pdb/data/structures/dividedThis is the entry point for a user finding a structure. This directory contains the current PDB, in pdb, mmCIF, XML, nmr_restraint, and structure_factors directories, with the files divided according to a two letter organization. Entries are grouped by the middle two characters of the ident code. For example, entry file pdb1abc.ent can be found in pub/pdb/data/structures/divided/pdb/ab
/pub/pdb/data/structures/modelsTheoretical model files that are maintained separately from the main archive
/pub/pdb/data/structures/obsoleteStructures and associated data files no longer part of the archive
/pub/pdb/derived_dataPlain text files that list information derived from all PDB entries, such as all PDB sequences in FASTA format.
/pub/pdb/docDocumentation, including file format descriptions and RCSB PDB Newsletters

Other downloads offered by RCSB PDB

Some of the http links above are also available in a short style (e.g. /download/4hhb.cif.gz). Additionally, for the short style links 2 URLs are available:

  • view: The HTTP/HTTPS response headers to the client are set with: Content-Type: text/plain
  • download: The HTTP/HTTPS response headers to the client are set with: Content-Type: application/octet-stream and Content-Transfer-Encoding: binary

PDB entry files

PDB entry files are available in several file formats (PDB, PDBx/mmCIF, XML, BinaryCIF), compressed or uncompressed, and with an option to download a file containing only "header" information (summary data, no coordinates).

File FormatActionStorage CompressionExample URL
Biological Assembly File in PDBDownloadUncompressedhttps://files.rcsb.org/download/1hh3.pdb1
Biological Assembly File in PDBDownloadCompressedhttps://files.rcsb.org/download/1hh3.pdb1.gz
Biological Assembly File in PDBx/mmCIFDownloadUncompressedhttps://files.rcsb.org/download/5a9z-assembly1.cif
Biological Assembly File in PDBx/mmCIFDownloadCompressedhttps://files.rcsb.org/download/5a9z-assembly1.cif.gz
PDBDownloadCompressedhttps://files.rcsb.org/download/4hhb.pdb.gz
PDBDownloadUncompressedhttps://files.rcsb.org/download/4hhb.pdb
PDBx/BinaryCIFDownloadCompressedhttps://models.rcsb.org/4hhb.bcif.gz
PDBx/BinaryCIFDownloadUncompressedhttps://models.rcsb.org/4hhb.bcif
PDBx/mmCIFDownloadCompressedhttps://files.rcsb.org/download/4hhb.cif.gz
PDBx/mmCIFDownloadUncompressedhttps://files.rcsb.org/download/4hhb.cif
XMLDownloadCompressedhttps://files.rcsb.org/download/4hhb.xml.gz
XMLDownloadUncompressedhttps://files.rcsb.org/download/4hhb.xml
XML (header only)DownloadCompressedhttps://files.rcsb.org/download/4hhb-noatom.xml.gz
XML (header only)DownloadUncompressedhttps://files.rcsb.org/download/4hhb-noatom.xml
Biological Assembly File in PDBViewUncompressedhttps://files.rcsb.org/view/1hh3.pdb1
Biological Assembly File in PDBx/mmCIFViewUncompressedhttps://files.rcsb.org/view/5a9z-assembly1.cif
PDBViewUncompressedhttps://files.rcsb.org/view/4hhb.pdb
PDB (header only)ViewUncompressedhttps://files.rcsb.org/header/4hhb.pdb
PDBx/mmCIFViewUncompressedhttps://files.rcsb.org/view/4hhb.cif
PDBx/mmCIF (header only)ViewUncompressedhttps://files.rcsb.org/header/4hhb.cif
XML (header only)ViewUncompressedhttps://files.rcsb.org/view/4hhb-noatom.xml

Small molecule files

Small molecule files, including the ligands/chemical components maintained in the Chemical Component Dictionary and the Biologically Interesting Molecule Reference Dictionary (BIRD) are available in multiple formats.

TypeFormatActionExample URL
BIRD atom representationCIFDownloadhttps://files.rcsb.org/birds/download/PRDCC_000001.cif
BIRD definitionCIFDownloadhttps://files.rcsb.org/birds/download/PRD_000001.cif
DefinitionCIFDownloadhttps://files.rcsb.org/ligands/download/HEM.cif
DefinitionXMLDownloadhttps://files.rcsb.org/ligands/download/HEM.xml
Ideal coordinatesSDFDownloadhttps://files.rcsb.org/ligands/download/HEM_ideal.sdf
Ideal coordinatesMOL2Downloadhttps://files.rcsb.org/ligands/download/HEM_ideal.mol2
Model coordinatesSDFDownloadhttps://files.rcsb.org/ligands/download/HEM_model.sdf
Model coordinatesMOL2Downloadhttps://files.rcsb.org/ligands/download/HEM_model.mol2
BIRD atom representationCIFViewhttps://files.rcsb.org/birds/view/PRDCC_000001.cif
BIRD definitionCIFViewhttps://files.rcsb.org/birds/view/PRD_000001.cif
Chemical Component InstanceSDFViewhttps://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=sdf
Chemical Component InstanceMOLViewhttps://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol
Chemical Component InstanceMOL2Viewhttps://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol2
DefinitionCIFViewhttps://files.rcsb.org/ligands/view/HEM.cif
DefinitionXMLViewhttps://files.rcsb.org/ligands/view/HEM.xml
Ideal coordinatesSDFViewhttps://files.rcsb.org/ligands/view/HEM_ideal.sdf
Ideal coordinatesMOL2Viewhttps://files.rcsb.org/ligands/view/HEM_ideal.mol2
Model coordinatesSDFViewhttps://files.rcsb.org/ligands/view/HEM_model.sdf
Model coordinatesMOL2Viewhttps://files.rcsb.org/ligands/view/HEM_model.mol2

Experimental data files and 3DEM maps

This table includes structure factors, NMR constraints, chemical shifts, electron density maps and map coefficient files.

File FormatActionStorage CompressionExample URL
Chemical ShiftsDownloadCompressedhttps://files.rcsb.org/download/2n2z_cs.str.gz
Chemical ShiftsDownloadUncompressedhttps://files.rcsb.org/download/2n2z_cs.str
NMR RestraintsDownloadCompressedhttps://files.rcsb.org/download/108d.mr.gz
NMR RestraintsDownloadUncompressedhttps://files.rcsb.org/download/108d.mr
NMR Restraints v2DownloadCompressedhttps://files.rcsb.org/download/108d_mr.str.gz
NMR Restraints v2DownloadUncompressedhttps://files.rcsb.org/download/108d_mr.str
Chemical ShiftsViewUncompressedhttps://files.rcsb.org/view/2n2z_cs.str
NMR RestraintsViewUncompressedhttps://files.rcsb.org/view/108d.mr
NMR Restraints v2ViewUncompressedhttps://files.rcsb.org/view/108d_mr.str
Structure FactorsDownloadCompressedhttps://files.rcsb.org/download/1btn-sf.cif.gz
Structure FactorsDownloadUncompressedhttps://files.rcsb.org/download/1btn-sf.cif
Structure FactorsViewUncompressedhttps://files.rcsb.org/view/1btn-sf.cif
Electron Density 2Fo-Fc Map (with fixed grid spacing at "high resolution/3") - DSN6 formatDownloadUncompressedhttps://edmaps.rcsb.org/maps/6dil_2fofc.dsn6
Electron Density Fo-Fc Map (with variable grid spacing from "high resolution/3" to "high resolution/2") - DSN6 formatDownloadUncompressedhttps://edmaps.rcsb.org/maps/6dil_fofc.dsn6
Electron Density Map Coefficients (MTZ format)DownloadUncompressedhttps://edmaps.rcsb.org/coefficients/6dil.mtz
Electron Density 2Fo-Fc & Fo-Fc Map (might be downsampled) - BinaryCIF formatDownloadUncompressedhttps://maps.rcsb.org/x-ray/6dil/cell/

Sequence data

Sequence data in FASTA format (full deposited sequence as in SEQRES records).

Please note that the FASTA download service at URL /pdb/download/downloadFastaFiles.do?structureIdList=4hhb&compressionType=uncompressedhas been discontinued. Users will need to migrate to the new endpoints below. Note that the output of the new endpoints are per entity (with chain identifiers provided in header) instead of per chain.

FASTA sequences per PDB entryDownloadUncompressed/fasta/entry/4HHB/download
FASTA sequence per polymer entity (identified by <pdb_id>_<entity_id>)DownloadUncompressed/fasta/entity/4HHB_1/download
FASTA sequence per polymer entity instance (chain) (identified by <pdb_id>.<asym_id>, please note this is the label_asym_id and not the author chain id)DownloadUncompressed/fasta/chain/4HHB.A/download

Sequence clusters data

Results of the weekly clustering of protein sequences in the PDB by MMseqs2 at 30%, 40%, 50%, 70%, 90%, 95%, and 100% sequence identity. Note that these files use polymer entity identifiers, instead of chain identifiers to avoid redundancy. The files are plain text with one cluster per line, sorted from largest cluster to smallest.

FileTypeStorage CompressionURL
Sequence clusters at <identity> % sequence identity clusteringDownloadUncompressedhttps://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-<identity>.txt

Holdings data

PDB id holdings data in json format. For more information, see the data API documentation.

FileTypeStorage CompressionURL
All current PDB idsDownloadUncompressedhttps://data.rcsb.org/rest/v1/holdings/current/entry_ids
All unreleased PDB idsDownloadUncompressedhttps://data.rcsb.org/rest/v1/holdings/unreleased/entry_ids
All removed PDB ids (obsoleted entries or theoretical models)DownloadUncompressedhttps://data.rcsb.org/rest/v1/holdings/removed/entry_ids

Chemical Component Dictionary (CCD) Data

A subset of properties is provided for all components from the Chemical Component Dictionary (CCD) which describes chemical properties of all molecules in the PDB archive. The atom file (cca.bcif) provides the following CIF columns: atom_id, comp_id, charge, and pdbx_stereo_config. The bond file (ccb.bcif) provides the following CIF columns: atom_id_1, atom_id_2, comp_id, molstar_protonation_variant, pdbx_aromatic_flag, pdbx_stereo_config, and value_order.

This data can be used by the Mol* ModelServer.

FileFormatActionURL
Chemical Component Atom DataBinaryCIFDownloadhttps://models.rcsb.org/cca.bcif
Chemical Component Bond DataBinaryCIFDownloadhttps://models.rcsb.org/ccb.bcif


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Last updated: 5/4/2022