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New Syntax for PDB DOIs for Entries Released After July 21, 2027

04/28 wwPDB News

On July 21, 2027, the wwPDB will fully transition to extended 12-character PDB IDs, the PDBx/mmCIF format, and the re-organized PDB archive. At this point, new 4-character IDs will no longer be issued.

PDB Digital Object Identifiers (DOI) can be used to link to the corresponding wwPDB DOI landing page. DOIs are unique, persistent alphanumeric string assigned to digital objects to provide a permanent, reliable link to their location online. DOIs will not change once assigned.

The DOI syntax for PDB entries after July 20, 2027 will reflect the extended PDB ID.

DOIs for PDB entries deposited after July 20, 2027 (only assigned 12-character PDB IDs)

PDB entries that will only be issued extended PDB IDs (e.g., pdb_1000axyz), will have the same PDB ID in both `_database_2.database_code` and `_database_2.pdbx_database_accession` data items.

These entries will have a new PDB DOI format based on the extended PDB ID, e.g., 10.2210/pdb_1000axyz/pdb.

All 12 characters, including the pdb_ prefix, are included.

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB pdb_1000axyz pdb_1000axyz 10.2210/pdb_1000axyz/pdb

DOIs for PDB entries deposited before July 21, 2027 (assigned both 4- and 12-character PDB IDs)

The PDB DOI, 4-character PDB ID, and extended 12-character PDB ID are stored in the `database_2` category of the PDBx/mmCIF model file:

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 1ABC pdb_00001abc 10.2210/pdb1abc/pdb

For these entries, the PDB DOI format with “pdb” prefix remains unchanged, e.g., 10.2210/pdb1abc/pdb.

For example, the PDB entry with ID 8y9m (and extended PDB ID pdb_00008y9m) has the DOI https://doi.org/10.2210/pdb8y9m/pdb.

Citing PDB DOIs

Many journals use PDB DOIs to link to PDB data from published articles.

PDB DOIs are also used as citations for entries that are not associated with a primary citation.

  • PDB DOIs are also used as citations for entries that are not associated with a primary citation.
  • Entries that have been issued a 4-character ID (meaning it has been deposited before July 21, 2027) should be cited using the ID and DOI syntax for 4-character IDs (e.g., 10.2210/pdb1abc/pdb). This includes structures with extended IDs created from 4-character IDs using the prefix “pdb_0000” (e.g., “2abc” for pdb_00002abc)
  • Entries that have only been issued a 12-character ID (meaning it has been deposited after July 20, 2027) should be cited using the new ID and DOI syntax (e.g., 10.2210/pdb_1000axyz/pdb)

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

Transition Resources

<I>PDB entries deposited after July 20, 2027 will only be assigned extended PDB IDs and will follow a new DOI syntax.</I>PDB entries deposited after July 20, 2027 will only be assigned extended PDB IDs and will follow a new DOI syntax.

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