Dear all,
As announced previously, wwPDB, in collaboration with thePDBx/mmCIF
Working Group <https://www.wwpdb.org/task/mmcif>, 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
<https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d>:
https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d)
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,
seehttps://github.com/wwPDB/extended-wwPDB-identifier-examples. To learn
about PDBx/mmCIF, please visithttps://mmcif.wwpdb.org/.
For any further information please contact us ati...@wwpdb.org.
Read this news on the wwPDB website:
https://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7
Kind regards,
Deborah.
--
-------------------------------------------------------------------
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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