[3dem] Future Planning: PDB entries with extended CCD or PDB IDs will be distributed in the PDBx/mmCIF format only

[Justin Flatt]

wwPDB, in collaboration with the PDBx/mmCIF Working Group [1], has set 
plans to extend the length of accession codes (IDs) for PDB and Chemical 
Component Dictionary (CCD) entries in the future. PDB entries containing 
these extended IDs will not be supported by the legacy PDB file format. 
(see previous announcement [2])

CCD ID EXTENSION

CCD entries are currently identified by unique three-character 
alphanumeric IDs. At current growth rates, we anticipate running out of 
three-character IDs before 2024. After this point, the wwPDB will issue 
five-character alphanumeric accession codes for CCD IDs in the OneDep 
system. To avoid confusion with current four-character PDB IDs, 
four-character codes will not be used. Owing to limitations of the 
legacy PDB file format, PDB entries containing the new five character ID 
codes will only be distributed in PDBx/mmCIF format.

In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG 
that will never be used in the PDB. These reserved codes can be used for 
new ligands during structure determination so that they can be 
identified as new upon deposition and added to the CCD during 
biocuration.

PDB ID EXTENSION

wwPDB will be extending PDB ID length to eight characters prefixed by 
'pdb', e.g., pdb_00001abc. Each PDB entry has a corresponding Digital 
Object Identifier (DOI), often required for manuscript submission to 
journals and described in publications by the structure authors. 
Extended PDB IDs and corresponding PDB DOIs have been included in the 
PDBx/mmCIF formatted atomic coordinate files for all new and re-released 
entries since August 2021.

For example, PDB entry issued with 4-character PDB ID, 1abc, will have 
the extended PDB ID (pdb_00001abc) and corresponding PDB DOI 
(10.2210/pdb1abc/pdb), as listed in the _database_2 PDBx/mmCIF category.

  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 example, PDB entry issued with 8-character PDB ID, pdb_00099xyz, 
after all 4-character IDs are consumed:

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB pdb_00099xyz pdb_00099xyz 10.2210/pdb_00099xyz/pdb

After all four-character PDB IDs are consumed, newly-deposited PDB 
entries will only be issued extended PDB ID codes, and PDB entries will 
only be distributed in PDBx/mmCIF format. PDB entries with 
four-character PDB IDs will remain unchanged.

RESOURCES

wwPDB is asking users and software developers to review their code and 
remove any current limitations on PDB and CCD ID lengths, and to enable 
use of PDBx/mmCIF format files. Example files with extended PDB and/or 
CCD IDs are available via github to assist code revisions, see 
https://urldefense.com/v3/__https://github.com/wwPDB/extended-wwPDB-identifier-examples__;!!Mih3wA!B4YvJUz5E_tp3K5gRGm9hSCFJbWzs-lr-frb1Ix7iiIDyJHTzQiHlsZ-hPV2hWxYJ8TWMoZDXl3tU0lQ71kBnTBm$  . To learn 
about PDBx/mmCIF, please visit https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!B4YvJUz5E_tp3K5gRGm9hSCFJbWzs-lr-frb1Ix7iiIDyJHTzQiHlsZ-hPV2hWxYJ8TWMoZDXl3tU0lQ7wBT230V$  .

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

Links:
------
[1] https://urldefense.com/v3/__https://www.wwpdb.org/task/mmcif__;!!Mih3wA!B4YvJUz5E_tp3K5gRGm9hSCFJbWzs-lr-frb1Ix7iiIDyJHTzQiHlsZ-hPV2hWxYJ8TWMoZDXl3tU0lQ72lZaUnB$  
[2] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2021*607760112786e73a79c76f9d__;Iw!!Mih3wA!B4YvJUz5E_tp3K5gRGm9hSCFJbWzs-lr-frb1Ix7iiIDyJHTzQiHlsZ-hPV2hWxYJ8TWMoZDXl3tU0lQ7xXQ9ngw$  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20220907/20199af1/attachment.html>