Transitioning to PDBx/mmCIF and Extended PDB IDs

News

Transitioning to PDBx/mmCIF and Extended PDB IDs

07/15

wwPDB strongly encourages all users to adopt the extended PDB ID format and transition to PDBx/mmCIF file format as soon as possible. This includes making changes to software; referring to structures by the full 12-character ID in all communications; and encouraging your communities to do the same.

Transitioning to Extended PDB IDs

As the PDB archive continues to expand, the four-character PDB accession codes (PDB IDs) are expected to be fully assigned before 2028. To support the growth of the archive, the wwPDB has extended the length of PDB IDs to 12 alphanumeric characters including "pdb_" prefix (e.g., "1abc" will become "pdb_00001abc", case insensitive) to improve text mining capabilities in the published literature. Users or journals will be able to parse/recognize PDB IDs using the prefix “pdb_”. The prefix and zeros must be included in the extended PDB ID.

Once four-character PDB IDs are fully assigned, new entries will only receive extended PDB IDs; data will not be provided in the legacy PDB file format files.

Access further details, including a transition plan, example files, and supporting FAQs at wwPDB: Extended PDB ID With 12 Characters.

Users can adopt usage of extended PDB IDs for all PDB entries immediately using the _database_2.pdbx_database_accession data item in the PDBx/mmCIF formatted structure files.

For example:

 loop_ 
 _database_2.database_id 
 _database_2.database_code 
 _database_2.pdbx_database_accession 
 _database_2.pdbx_DOI 
 PDB 2HYV pdb_00002hyv 10.2210/pdb2hyv/pdb 
 WWPDB D_1000038924 ? ?

New PDB DOI Format

All existing PDB entries with four-character PDB IDs issued have DOI formatted as 10.2210/pdb[4-character_PDB_ID]/pdb that resolve to the corresponding wwPDB DOI landing page. For example, PDB entry 8y9m (pdb_00008y9m) has the DOI https://doi.org/10.2210/pdb8y9m/pdb. Importantly, this DOI will remain unchanged in the future.

When all 4-character PDB IDs have been exhausted, all new PDB entries will be issued extended PDB IDs issued and a NEW DOI formatted as 10.2210/[Extended_PDB_ID]/pdb that will resolve to the corresponding wwPDB DOI landing page. For example, PDB entry “pdb_10001xyz” will have the DOI https://doi.org/10.2210/pdb_10001xyz/pdb.

Transitioning to PDBx/mmCIF Format

To help users adopt extended PDB ID and PDBx/mmCIF file format, wwPDB offers an mmCIF User Guide and software resources such as mmCIF parsers and CIF Editor.

In addition, wwPDB will provide a Beta PDB Archive organized by extended PDB ID (including file naming, directories, and datablock naming) in early 2026. The current PDB archive organizes data files grouped by data type, e.g., coordinates, experimental data, assemblies, validation reports, etc.

A major change in the Beta PDB archive will be the re-organization of file directory at entry level, following the same file organization as the PDB Versioned Archive. In other words, all the data files associated to an entry will be grouped together under its PDB ID (extended PDB ID) with two letter hash. Please watch wwPDB.org and community bulletin boards for announcements on the file organization for the Beta PDB archive later this year.

We recommend users fully adopt all of these these changes before the end of 2026. Early adoption will contribute to the long-term sustainability and interoperability of 3D biostructure data across the scientific community.

In particular, journals should begin adopting the Extended PDB ID format (in Text, Tables, and Data Availability Statements), updating links included in journal articles for PDB IDs to the wwPDB DOI landing page via CrossRef, and verifying software tools linked from a journal article (e.g., FirstGlance or Jsmol for 3D visualization) support of extended PDB IDs and PDBx/mmCIF.

Should you have any questions or require further assistance, please do not hesitate to contact us at info@wwpdb.org. We greatly appreciate your support and cooperation as we work together to enhance the future of structural data accessibility.