# RCSB Protein Data Bank License: permissive (CC0-1.0); Mdexa hosting: link-only. all parts permissive; conditions are the union of the parts - Commercial use: Yes · Derivatives: Yes · Redistribution: Yes · File on Mdexa: No - License status: Permissive (CC0-1.0) - Mdexa hosting: Link only — License permissive: all parts permissive; conditions are the union of the parts. Link only. - Last verified: 2026-11-14 - Card: https://mdexa.com/datasets/rcsb-pdb/ ## Key facts - Domain: Genomics and omics - Content type: Databases - Size: — - Language: English - Modality: Text - Publisher: RCSB PDB (wwPDB) - Year: 1971 ## Commercial use of RCSB Protein Data Bank - Commercial use: Yes. The overall verdict takes the strictest part; the parts carry different licenses, listed below. - License status: Permissive. - Conditions: Attribution, Notice kept - License part: data files contained in the PDB archive — Permissive (CC0-1.0) - License part: RCSB PDB programmatic APIs — Permissive (CC0-1.0) - License part: RCSB PDB software products — Permissive (Apache-2.0) - License part: Molecule of the Month illustrations — Permissive (CC-BY-4.0) - License part: PDB-101 content — Permissive (CC-BY-4.0) - License part: Other RCSB.org content — Permissive (CC-BY-4.0) Verdicts record what sources state and are not legal advice. ## RCSB Protein Data Bank license evidence all parts permissive; conditions are the union of the parts - **Terms of use page** — CC0-1.0: Statement found in snapshot s02 (page) — "The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Univer" — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page**: Statement found in snapshot s02 (page) — "Data provided by RCSB PDB programmatic APIs are available under the same license unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page**: Statement found in snapshot s02 (page) — "RCSB PDB software products are distributed under the terms of an open source license ( MIT or Apache 2.0 )." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page**: Statement found in snapshot s02 (page) — "Molecule of the Month articles are copyrighted by RCSB PDB and the article authors. Text can be reprinted with permission, with attribution, and without the right to manipulate or change content." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page** — CC-BY-4.0: Statement found in snapshot s02 (page) — "Molecule of the Month illustrations are available under a CC-BY-4.0 license ." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page** — CC-BY-4.0: Statement found in snapshot s02 (page) — "PDB-101 content is free for use under a CC-BY-4.0 license" — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page**: Statement found in snapshot s02 (page) — "Global Health articles are copyrighted by RCSB PDB and the article authors." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Terms of use page** — CC-BY-4.0: Statement found in snapshot s02 (page) — "Other RCSB.org content ( e.g. , user guide documentation, statistics graphs, other screenshots) is available under a CC-BY-4.0 license ." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) - **Dataset page**: Part "integrated external resource" found in snapshot s02 (page) — "unless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed." — https://www.rcsb.org/pages/policies (2026-11-12; Page opened) ## Source and lineage — ## Known issues with RCSB Protein Data Bank — ## Preflight Not run (data not ingested). ## Downloading RCSB Protein Data Bank and API access Mdexa does not serve files. Original source: - https://www.rcsb.org/ - https://www.rcsb.org/pages/policies ### Access recipe - Atomic coordinates · https://files.wwpdb.org/pub/pdb/data/structures/ - X-ray data: Structure Factors · https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/ - NMR data: Restraints and chemical shifts · https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/ - NMR chemical shifts · https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/ - Small molecules references: CCD · https://files.wwpdb.org/pub/pdb/refdata/chem_comp/ - Small molecules references: BIRD · https://files.wwpdb.org/pub/pdb/refdata/bird - Assemblies (mmCIF) · https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/ - Assemblies (PDB) · https://files.wwpdb.org/pub/pdb/data/biounit/PDB/ - Archive holdings · https://files.wwpdb.org/pub/pdb/holdings/ - RCSB PDB coordinate files in PDB Exchange Format (mmCIF) · https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF - RCSB PDB coordinate files in PDBML format · https://files.rcsb.org/pub/pdb/data/structures/divided/XML - RCSB PDB coordinate files in PDB format · https://files.rcsb.org/pub/pdb/data/structures/divided/pdb - Bulk download: `rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF` - Bulk download: `rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/XML/ ./XML` - Bulk download: `rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/pdb/ ./pdb` - Bulk download: `rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp/validation_reports/ ./validation_reports` - Bulk download: `aws s3 sync s3://pdbsnapshots/ ./local-directory/ --no-sign-request` - Bulk download: `aws s3 sync s3://pdbsnapshots/20250101/ ./local-directory/20250101 --no-sign-request` ## Citing RCSB Protein Data Bank No recommended citation text. - 10.1093/nar/28.1.235 - 10.1093/nar/gkae1091 - 10.1093/nar/gky949 ## Machine-readable - JSON: https://mdexa.com/datasets/rcsb-pdb.json - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-14 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Re-adjudicated under the current rules; all machine checks still pass. - 2026-11-13 Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions). ## Practical information ### Content scope - Since 1971 the PDB archive has been described as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. > Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. https://www.wwpdb.org/ (2026-11-13) - Coordinate sets produced by X-ray crystallography, NMR, electron microscopy, neutron diffraction, powder diffraction, and fiber diffraction can be deposited to the PDB, provided the molecule studied meets the minimum size requirement. > Currently, coordinate sets produced by X-ray crystallography, NMR, electron microscopy, neutron diffraction, powder diffraction, and fiber diffraction can be deposited to the PDB, provided the molecule studied meets the minimum size requirement. https://www.wwpdb.org/documentation/policy (2026-11-13) ### Identifiers - PDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors. > PDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors. https://www.rcsb.org/pages/policies (2026-11-12) - The core_entry object covers a PDB entry or Computed Structure Model and is identified by an entry_id, which can be an alphanumeric PDB-ID or a CSM-ID starting with AF_ or MA_. > core_entry : data that relates to a PDB entry or Computed Structure Model (CSM). Identified by an entry_id, which can be an alphanumeric PDB-ID or a CSM-ID that starts with AF_ or MA_ https://www.rcsb.org/docs/programmatic-access/web-apis-overview (2026-11-13) - The core_chem_comp object is a chemical component identified by a unique alphanumeric code chem_comp_id. > core_chem_comp : a chemical component. Identified by a unique alphanumeric code chem_comp_id https://www.rcsb.org/docs/programmatic-access/web-apis-overview (2026-11-13) - The Sequence Coordinates API provides alignments between structural and sequence databases, with alignment data available for NCBI RefSeq, UniProt and PDB sequences. > The Sequence Coordinates API provides alignments between structural and sequence databases and integrates protein positional features from multiple resources. Alignment data is available for NCBI RefSeq (including protein and genomic sequences), UniProt and PDB sequences. https://www.rcsb.org/docs/programmatic-access/web-apis-overview (2026-11-13) ### Access - Web API: https://www.rcsb.org/docs/programmatic-access/web-apis-overview - Bulk download: https://files.wwpdb.org - Web API: https://www.rcsb.org/docs/programmatic-access/file-download-services ### Versions - The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC. > The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC. https://www.wwpdb.org/ftp/pdb-ftp-sites (2026-11-13) - PDB entries deposited on or after July 21, 2027 will use the 12-character PDB ID DOI format 10.2210/pdb_1000axyz/pdb. > PDB entries deposited on or after July 21, 2027 , will use the 12-character PDB ID DOI format 10.2210/pdb_1000axyz/pdb (where pdb_1000axyz is the 12-character PDB ID). https://www.rcsb.org/pages/policies (2026-11-12) - The legacy RCSB REST search and fetch APIs were shut down on 9 December 2020 in favour of the Search and Data APIs. > legacy RCSB PDB APIs (REST search and fetch) will be discontinued on December 9, 2020 as announced previously. https://www.rcsb.org/news/5fc9176809ae2a096d081e28 (2026-11-13) - wwPDB deprecated the FTP download protocol on 1 November 2024; HTTPS and rsync remain. > wwPDB plans to deprecate FTP download protocol on November 1st 2024 https://pdbj.org/news/Deprecation_FTP_Nov2024 (2026-11-13) - Large structures that used to be split across several PDB-format files were merged into single entries at the end of 2014. > Historically, large files containing >62 chains and/or 99999 ATOM lines were "split" across multiple PDB format files. These files were combined into single entries at the end of 2014 https://www.rcsb.org/docs/general-help/structures-without-legacy-pdb-format-files (2026-11-13) ### Known defects and misuse - The page states that structures determined before experimental data deposition became mandatory may have no available experimental data, and that such structures are difficult to validate without it. > On occasion, the wwPDB is asked to archive a structure that was determined before deposition of experimental data became mandatory and the experimental data are no longer available. It is difficult to validate such structures without experimental data. https://www.wwpdb.org/documentation/policy (2026-11-13) - RCSB: X-ray ligands without deposited structure factors (typically before 2008) cannot be checked for fit to experimental data. > ligands in X-ray structures lacking associated structure factor data (typically deposited prior to 2008), as goodness-of-fit to the experimental data cannot be calculated without structure factor data. https://www.rcsb.org/docs/general-help/ligand-structure-quality-in-pdb-structures (2026-11-13) - wwPDB: when experimental data change, a new entry with a new ID replaces the old one, which is obsoleted but stays in the archive. > The old entry is then obsoleted (if the depositor wishes) and replaced (superseded) by the new one. https://www.wwpdb.org/documentation/policy (2026-11-13) - Buttenschoen, Morris and Deane (PoseBusters) report that deep-learning docking methods trained on PDB-derived sets often produce physically implausible poses, and that RMSD alone is not a sufficient evaluation. > It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode. https://europepmc.org/article/MED/38425520 (2026-11-13) ### Suited for - The page states that annual archive snapshots may be used to provide a stable set of entries for analysis and to show changes introduced by wwPDB remediation efforts. > The annual archive snapshots provide the data in the archive at the start of each year or at selected milestone moments. These data may be used to provide a stable set of entries for analysis and allow users to see changes introduced due to remediation efforts by wwPDB. https://www.wwpdb.org/ftp/pdb-ftp-sites (2026-11-13) - RCSB states that computed structure models can serve as starting models for proteins and complexes whose structures have not been determined experimentally. > Yet CSMs can provide great starting models for the millions of proteins and their complexes whose structures have not been experimentally determined. https://www.rcsb.org/docs/general-help/computed-structure-models-and-rcsborg (2026-11-13) ### Not suited for - Theoretical model depositions determined purely in silico, for example by homology or ab initio methods, are no longer accepted. > Theoretical model depositions determined purely in silico using, for example, homology or ab initio methods, are no longer accepted. https://www.wwpdb.org/documentation/policy (2026-11-13) - The page directs that crystal structures of peptides with fewer than 24 residues within any polymer chain that do not meet the stated criteria be deposited at the Cambridge Crystallographic Data Centre. > Crystal structures of peptides with fewer than 24 residues within any polymer chain that do not meet the criteria above should be deposited at the Cambridge Crystallographic Data Centre https://www.wwpdb.org/documentation/policy (2026-11-13) ### No sourced statement yet Latest version, Commercial licensing ## Continue in this database This record is one of 109 processed and verified records (datasets, data resources and open models). To find others, call `https://mcp.mdexa.com/v1/datasets?q=` or connect the MCP server at `https://mcp.mdexa.com/mcp`; no key is needed for 20 calls per minute. Rows are under 1 KB; an empty result means "not listed". For a list of items, one batch check (free account) returns a report. Guide: /agents.md. Similar records: AlphaFold Protein Structure Database (https://mdexa.com/datasets/alphafold-db/); GEO (https://mdexa.com/datasets/geo/); gnomAD (https://mdexa.com/datasets/gnomad/).