RCSB PDB Help
Programmatic Access
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). Since February 01 2023, the wwPDB enriches PDB entries with additional annotation and distributes the latest versions of each entry via next generation archive (NextGen) accessible at files-nextgen.wwpdb.org.
In addition to experimental structures, the PDB archive includes structures determined by integrative and hybrid structure determination methods (IHM). Users can access and download IHM structures and associated data at files.wwpdb.org/pub/pdb_ihm/.
All data are available via the HTTPS protocol. Note that the FTP protocol is no longer supported. See the announcement.
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.
File Access URLs
DNS names are required for programmatic access to PDB archive downloads:
- HTTPS: https://files.wwpdb.org
- RSYNC: rsync://rsync.rcsb.org
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:
- ftp://snapshots.rcsb.org/rsyncSnapshots.sh To make a local copy of an annual snapshot or sections of the snapshot. This script is annotated to assist in downloading only sections of the archive.
- https://files.wwpdb.org/pub/pdb/software/rsyncPDB.sh To copy the current contents of the entire archive
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 PDB archive downloads.
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 |
| /pub/pdb/validation_reports | Validation reports files in mmCIF, PDF and XML formats and supporting data |
| /pub/pdb_ihm/data/entries/ | Structures determined by integrative and hybrid structure determination methods (IHM) and associated data files |
| /pub/pdb_ihm/holdings/ | Current PDB-IHM holdings, released IHM structures last modified dates, unreleased IHM entries |
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.
Experimental data files and 3DEM maps
This table includes structure factors, NMR constraints, chemical shifts, electron density maps and map coefficient files.
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://files.rcsb.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 |
