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RCSB Protein Data Bank

Verified by Mdexa · Checked against the source text under public rules.How we check

Commercial use
Yes
Derivatives
Yes
Redistribution
Yes
File on Mdexa
NoLink only

all parts permissive

PermissiveLink onlyCC0-1.0Save

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Mdexa verified · Permissive · 2026-11Mdexa verifiedPermissive · 2026-11

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Cite this pageMdexa, RCSB Protein Data Bank, https://mdexa.com/datasets/rcsb-pdb/, verified 2026-11-14.

Key facts

Domain
Genomics and omics Modern medicine
Content
DatabasesRCSB PDB enables scientific breakthroughs via tools for searching, visualization, and analysis of 3D structural data, and is a member of the Worldwide PDB partnership.
Size
—
Language / modality
English / Text
Publisher
RCSB PDB (wwPDB)
Year
1971
Expert review
—
Verification
Verified: license text seen

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)

Quoted statements and their sources are in RCSB Protein Data Bank license evidence.

Verdicts record what sources state and are not legal advice.

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.
    wwpdb.org ·
    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/ · Dataset page · checked 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.
    wwpdb.org ·
    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 · Terms of use page · checked 2026-11-13

Identifiers

  • PDB IDPDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors.
    rcsb.org ·
    PDB entries are assigned a PDB ID and are frequently described in a publication by the structure authors.

    https://www.rcsb.org/pages/policies · Terms of use page · checked 2026-11-12

  • entry_idThe 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_.
    rcsb.org ·
    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 · api-doc · checked 2026-11-13

  • chem_comp_idThe core_chem_comp object is a chemical component identified by a unique alphanumeric code chem_comp_id.
    rcsb.org ·
    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 · api-doc · checked 2026-11-13

  • → NCBI RefSeq and UniProtThe Sequence Coordinates API provides alignments between structural and sequence databases, with alignment data available for NCBI RefSeq, UniProt and PDB sequences.
    rcsb.org ·
    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 · api-doc · checked 2026-11-13

Access

  • Web APIrcsb.org JSON
    • Own terms: commercial use With conditions · redistribution With conditions
      rcsb.org ·
      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 · Terms of use page · checked 2026-11-12

    • All RCSB PDB APIs have rate limits in place; the page suggests starting with a handful of requests per second, and exceeding the limit returns a 429 HTTP error code indicating that the request rate must be reduced.
      rcsb.org ·
      all RCSB PDB APIs have rate limits in place. We recommend starting with a handful of requests per second. If you exceed the limit, the service will respond with a 429 HTTP error code, indicating that you need to reduce your request rate as described below.

      https://www.rcsb.org/docs/programmatic-access/web-apis-overview · api-doc · checked 2026-11-13

  • Bulk downloadfiles.wwpdb.org PDBx/mmCIF · XML · PDB

    Same terms as the card's license.

    • The FTP file download protocol in the PDB archive has been deprecated since November 1st 2024.
      wwpdb.org ·
      Please note that the FTP file download protocol in the PDB archive has been deprecated since November 1st 2024 ( announcement ).

      https://www.wwpdb.org/ftp/pdb-ftp-sites · Dataset page · checked 2026-11-13

  • Web APIrcsb.org

    Same terms as the card's license.

Versions

  • Update cycleThe PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.
    wwpdb.org ·
    The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.

    https://www.wwpdb.org/ftp/pdb-ftp-sites · Dataset page · checked 2026-11-13

  • Breaking changePDB entries deposited on or after July 21, 2027 will use the 12-character PDB ID DOI format 10.2210/pdb_1000axyz/pdb.
    rcsb.org ·
    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 · Terms of use page · checked 2026-11-12

  • Breaking changeThe legacy RCSB REST search and fetch APIs were shut down on 9 December 2020 in favour of the Search and Data APIs.
    rcsb.org ·
    legacy RCSB PDB APIs (REST search and fetch) will be discontinued on December 9, 2020 as announced previously.

    https://www.rcsb.org/news/5fc9176809ae2a096d081e28 · official-change-notice · checked 2026-11-13

  • Breaking changewwPDB deprecated the FTP download protocol on 1 November 2024; HTTPS and rsync remain.
    pdbj.org ·
    wwPDB plans to deprecate FTP download protocol on November 1st 2024

    https://pdbj.org/news/Deprecation_FTP_Nov2024 · official-change-notice · checked 2026-11-13

  • Breaking changeLarge structures that used to be split across several PDB-format files were merged into single entries at the end of 2014.
    rcsb.org ·
    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 · Dataset page · checked 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.
    wwpdb.org ·
    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 · Terms of use page · checked 2026-11-13

  • RCSB: X-ray ligands without deposited structure factors (typically before 2008) cannot be checked for fit to experimental data.
    rcsb.org ·
    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 · Dataset page · checked 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.
    wwpdb.org ·
    The old entry is then obsoleted (if the depositor wishes) and replaced (superseded) by the new one.

    https://www.wwpdb.org/documentation/policy · Dataset page · checked 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.
    europepmc.org ·
    It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode.

    https://europepmc.org/article/MED/38425520 · peer-reviewed-paper · checked 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.
    wwpdb.org ·
    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 · Dataset page · checked 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.
    rcsb.org ·
    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 · Dataset page · checked 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.
    wwpdb.org ·
    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 · Terms of use page · checked 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.
    wwpdb.org ·
    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 · Terms of use page · checked 2026-11-13

RCSB Protein Data Bank license evidence 9

Conditions are the union of the parts

  1. Terms of use pagePage opened
    CC0-1.0
    Third-party text · Terms of use pageThe wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Univer

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  2. Terms of use pagePage opened
    Third-party text · Terms of use pageData 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.

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  3. Terms of use pagePage opened
    Third-party text · Terms of use pageRCSB PDB software products are distributed under the terms of an open source license ( MIT or Apache 2.0 ).

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  1. Terms of use pagePage opened
    Third-party text · Terms of use pageMolecule 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.

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  2. Terms of use pagePage opened
    CC-BY-4.0
    Third-party text · Terms of use pageMolecule of the Month illustrations are available under a CC-BY-4.0 license .

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  3. Terms of use pagePage opened
    CC-BY-4.0
    Third-party text · Terms of use pagePDB-101 content is free for use under a CC-BY-4.0 license

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  4. Terms of use pagePage opened
    Third-party text · Terms of use pageGlobal Health articles are copyrighted by RCSB PDB and the article authors.

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  5. Terms of use pagePage opened
    CC-BY-4.0
    Third-party text · Terms of use pageOther RCSB.org content ( e.g. , user guide documentation, statistics graphs, other screenshots) is available under a CC-BY-4.0 license .

    Statement found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02
  6. Dataset pagePage opened
    Third-party text · Dataset pageunless they originate from an integrated external resource , in which case the licensing restrictions applied by the data provider must be followed.

    Part "integrated external resource" found in snapshot s02 (page)

    rcsb.org2026-11-12 · s02

Source and lineage

No upstream or downstream datasets recorded.

Known issues with RCSB Protein Data Bank

—

Preflight

Not run Runs only on ingested data; says nothing about quality.

Downloading RCSB Protein Data Bank and API access

No file on Mdexa (see the verdict). Get it from the source and confirm the terms there:

Citing RCSB Protein Data Bank

Mdexa, RCSB Protein Data Bank, https://mdexa.com/datasets/rcsb-pdb/, verified 2026-11-14.
More citation details

The source gives no citation text; the line above cites this card.

  • 10.1093/nar/28.1.235
  • 10.1093/nar/gkae1091
  • 10.1093/nar/gky949

Machine-readable

rcsb-pdb.jsonrcsb-pdb.mdcatalog.json

Change log 29
2026-11-14Known 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.
2026-11-14Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote.
2026-11-14Known 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.
2026-11-14Known 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.
2026-11-14Re-adjudicated under the current rules; all machine checks still pass.
2026-11-14Known 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.
2026-11-14Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Known 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.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Re-adjudicated under the current rules; all machine checks still pass.
2026-11-13Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions).

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