Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

01/08 

wwPDB anticipates that all the four character PDB accession codes (PDB ID) will be consumed by 2029.

With the continuous growth of PDB archive, wwPDB has revised the PDB accession code format by extending its length and prepending “PDB” (e.g., "1abc" will become "pdb_00001abc"). This process will enable text mining detection of PDB entries in the published literature and allow for more informative and transparent delivery of revised data files.

Entries with extended PDB IDs (12 characters) will not be compatible with the legacy PDB file format once four-character PDB IDs are consumed. wwPDB encourages scientific journals, PDB community and users to transition to using the PDBx/mmCIF format and the extended PDB ID format as soon as possible.

Resources are available to help PDB users with this transition through the wwPDB resource portal page (Extended PDB ID With 12 Characters). This page links to useful resources for handling this change, including an FAQ on PDB ID extension, materials to learn more about PDBx/mmCIF format, and links to other PDBx/mmCIF resources and software tools. As the transition phase progresses, more training resources will be added to this page.

Additionally, a PDB “beta” archive will be provided during the transition phase in 2026. The directory structure of this “beta” archive will mirror the data organization of the PDB Versioned Archive in the form of https://files-beta.org/pub/pdb/data/entries/two-letter-hash/pdb_accession_code/entry_data_File_names. The two-letter hash will be based on the n-2 and n-3 characters. For example, PDB entry PDB_12345678 will be under /67/. This will maintain consistency with the current PDB archive, where e.g. PDB entry 1abc is under /ab.

Once all the four character PDB accession codes are consumed, this PDB “beta” archive will become the PDB main archive and the current PDB archive will be removed.

Download example files containing extended PDB IDs for software adoption from GitHub.

wwPDB recently announced that PDB three-character Chemical Component IDs have been consumed. Five-character alphanumeric accession codes for CCD IDs are now issued by the OneDep system.

For any further information please contact us at info@wwpdb.org.

Sample extended PDB ID

New Features Index

• 05/27 Notice: NGL Viewer Deprecation

• 05/14 Switch from MMTF to BCIF

• 05/09 Announcement: EDMAPS.rcsb.org Shutdown

• 05/01 Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

• 04/30 wwPDB News: Coming soon: Annotation of Protein Modifications in the PDB

• 04/01 Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org

• 03/31 Explore Mechanism and Catalytic Site Annotations

• 03/29 Take the EDMAPS.rcsb.org Survey

• 03/24 Register for the April 1 Mol* Virtual Office Hour

• 03/12 wwPDB News: Paper Published on CryoEM Archiving and Validation Recommendations

• 02/25 Register for the March 28 Office Hour to Ask A Biocurator

• 02/12 Use a Python Package to Access the RCSB PDB Search API

• 01/30 Notice: NGL Viewer Deprecation

• 01/24 Take the CSM User Survey and Win

• 01/18 Undergrads: Spend your summer with RCSB PDB

• 01/15 Switch from MMTF to BCIF

• 01/08 wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

• 01/07 Applications Open for Director

• 01/03 wwPDB News: Time-stamped Copies of PDB and EMDB Archives