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, files.wwpdb.org (data download details) and the versioned archive, files-versioned.wwpdb.org (versioning details).

Protocols: HTTPS and FTP

All data are available via HTTPS and FTP. Note that FTP users should switch to binary mode before downloading data files. Note also that most web browsers (e.g., Chrome) have dropped support for FTP. You will need a separate FTP client for downloading via FTP protocol.

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. The FTP protocol will be gradually phased out.

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 same 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/mmCIF Biological assembly coordinate files in mmCIF format
/pub/pdb/data/biounit/PDB Biological assembly coordinate files in PDB format
/pub/pdb/data/monomers PDB Chemical Component Dictionary and other info on monomers
/pub/pdb/data/status Details of entries on hold and in processing
/pub/pdb/data/structures/all Analogous 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/divided This 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/models Theoretical model files that are maintained separately from the main archive
/pub/pdb/data/structures/obsolete Structures and associated data files no longer part of the archive
/pub/pdb/derived_data Plain text files that list information derived from all PDB entries, such as all PDB sequences in FASTA format.
/pub/pdb/doc Documentation, 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 Format Action Storage Compression Example URL
Biological Assembly File in PDB Download Uncompressed https://files.rcsb.org/download/1hh3.pdb1
Biological Assembly File in PDB Download Compressed https://files.rcsb.org/download/1hh3.pdb1.gz
Biological Assembly File in PDBx/mmCIF Download Uncompressed https://files.rcsb.org/download/5a9z-assembly1.cif
Biological Assembly File in PDBx/mmCIF Download Compressed https://files.rcsb.org/download/5a9z-assembly1.cif.gz
PDB Download Compressed https://files.rcsb.org/download/4hhb.pdb.gz
PDB Download Uncompressed https://files.rcsb.org/download/4hhb.pdb
PDBx/BinaryCIF Download Compressed https://models.rcsb.org/4hhb.bcif.gz
PDBx/BinaryCIF Download Uncompressed https://models.rcsb.org/4hhb.bcif
PDBx/mmCIF Download Compressed https://files.rcsb.org/download/4hhb.cif.gz
PDBx/mmCIF Download Uncompressed https://files.rcsb.org/download/4hhb.cif
XML Download Compressed https://files.rcsb.org/download/4hhb.xml.gz
XML Download Uncompressed https://files.rcsb.org/download/4hhb.xml
XML (header only) Download Compressed https://files.rcsb.org/download/4hhb-noatom.xml.gz
XML (header only) Download Uncompressed https://files.rcsb.org/download/4hhb-noatom.xml
Biological Assembly File in PDB View Uncompressed https://files.rcsb.org/view/1hh3.pdb1
Biological Assembly File in PDBx/mmCIF View Uncompressed https://files.rcsb.org/view/5a9z-assembly1.cif
PDB View Uncompressed https://files.rcsb.org/view/4hhb.pdb
PDB (header only) View Uncompressed https://files.rcsb.org/header/4hhb.pdb
PDBx/mmCIF View Uncompressed https://files.rcsb.org/view/4hhb.cif
PDBx/mmCIF (header only) View Uncompressed https://files.rcsb.org/header/4hhb.cif
XML (header only) View Uncompressed https://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.

Type Format Action Example URL
BIRD atom representation CIF Download https://files.rcsb.org/birds/download/PRDCC_000001.cif
BIRD definition CIF Download https://files.rcsb.org/birds/download/PRD_000001.cif
Definition CIF Download https://files.rcsb.org/ligands/download/HEM.cif
Ideal coordinates MOL2 Download https://files.rcsb.org/ligands/download/HEM_ideal.mol2
Ideal coordinates SDF Download https://files.rcsb.org/ligands/download/HEM_ideal.sdf
Model coordinates MOL2 Download https://files.rcsb.org/ligands/download/HEM_model.mol2
Model coordinates SDF Download https://files.rcsb.org/ligands/download/HEM_model.sdf
BIRD atom representation CIF View https://files.rcsb.org/birds/view/PRDCC_000001.cif
BIRD definition CIF View https://files.rcsb.org/birds/view/PRD_000001.cif
Chemical Component Instance SDF View https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=sdf
Chemical Component Instance MOL View https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol
Chemical Component Instance MOL2 View https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol2
Definition CIF View https://files.rcsb.org/ligands/view/HEM.cif
Ideal coordinates MOL2 View https://files.rcsb.org/ligands/view/HEM_ideal.mol2
Ideal coordinates SDF View https://files.rcsb.org/ligands/view/HEM_ideal.sdf
Model coordinates MOL2 View https://files.rcsb.org/ligands/view/HEM_model.mol2
Model coordinates SDF View https://files.rcsb.org/ligands/view/HEM_model.sdf

Experimental data files and 3DEM maps

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

File Format Action Storage Compression Example URL
Chemical Shifts Download Compressed https://files.rcsb.org/download/2n2z_cs.str.gz
Chemical Shifts Download Uncompressed https://files.rcsb.org/download/2n2z_cs.str
NMR Restraints Download Compressed https://files.rcsb.org/download/108d.mr.gz
NMR Restraints Download Uncompressed https://files.rcsb.org/download/108d.mr
NMR Restraints v2 Download Compressed https://files.rcsb.org/download/108d_mr.str.gz
NMR Restraints v2 Download Uncompressed https://files.rcsb.org/download/108d_mr.str
Chemical Shifts View Uncompressed https://files.rcsb.org/view/2n2z_cs.str
NMR Restraints View Uncompressed https://files.rcsb.org/view/108d.mr
NMR Restraints v2 View Uncompressed https://files.rcsb.org/view/108d_mr.str
Structure Factors Download Compressed https://files.rcsb.org/download/1btn-sf.cif.gz
Structure Factors Download Uncompressed https://files.rcsb.org/download/1btn-sf.cif
Structure Factors View Uncompressed https://files.rcsb.org/view/1btn-sf.cif
Electron Density 2Fo-Fc Map (with fixed grid spacing at "high resolution/3") - DSN6 format Download Uncompressed https://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 format Download Uncompressed https://edmaps.rcsb.org/maps/6dil_fofc.dsn6
Electron Density Map Coefficients (MTZ format) Download Uncompressed https://edmaps.rcsb.org/coefficients/6dil.mtz
Electron Density 2Fo-Fc & Fo-Fc Map (might be downsampled) - BinaryCIF format Download Uncompressed https://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 entry Download Uncompressed /fasta/entry/4HHB/download
FASTA sequence per polymer entity (identified by <pdb_id>_<entity_id>) Download Uncompressed /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) Download Uncompressed /fasta/chain/4HHB.A/download
Sequences in FASTA format for all entries in the PDB archive Download Compressed https://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz

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.

File Type Storage Compression URL
Sequence clusters at <identity> % sequence identity clustering Download Uncompressed https://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.

File Type Storage Compression URL
All current PDB ids Download Uncompressed https://data.rcsb.org/rest/v1/holdings/current/entry_ids
All unreleased PDB ids Download Uncompressed https://data.rcsb.org/rest/v1/holdings/unreleased/entry_ids
All removed PDB ids (obsoleted entries or theoretical models) Download Uncompressed https://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.

File Format Action URL
Chemical Component Atom Data BinaryCIF Download https://models.rcsb.org/cca.bcif
Chemical Component Bond Data BinaryCIF Download https://models.rcsb.org/ccb.bcif


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Last updated: 11/2/2022