PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats

JY
Jasmine Young
Wed, Dec 13, 2023 3:56 PM

Dear PDB-l,

The PDB three-character Chemical Component IDs are consumed and PDB has
begun issuing five-character alphanumeric accession codes for CCD IDs in
the OneDep system
. To avoid confusion with current four-character PDB
IDs, four-character codes are not used. Owing to limitations of the
legacy PDB file format, PDB entries containing the new five character ID
codes are distributed in PDBx/mmCIF and PDBML formats (see previous
announcement).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=2023#63ff72ccc031758bf1c30ff7).

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.

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.
https://github.com/wwPDB/extended-wwPDB-identifier-examplesExample files
with extended PDB and/or CCD IDs are available via GitHub to assist with
code revisions To learn about PDBx/mmCIF, please visit
https://mmcif.wwpdb.org/ https://www.wwpdb.org/news/mmcif.wwpdb.org/.

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

--
Regards,

Jasmine

---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320

---==========================

Dear PDB-l, The PDB three-character Chemical Component IDs are consumed and *PDB has begun issuing five-character alphanumeric accession codes for CCD IDs in the OneDep system*. To avoid confusion with current four-character PDB IDs, four-character codes are not used. Owing to limitations of the legacy PDB file format, PDB entries containing the new five character ID codes are distributed in PDBx/mmCIF and PDBML formats (see previous announcement).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=2023#63ff72ccc031758bf1c30ff7>). 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. 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. https://github.com/wwPDB/extended-wwPDB-identifier-examplesExample files with extended PDB and/or CCD IDs are available via GitHub to assist with code revisions To learn about PDBx/mmCIF, please visit https://mmcif.wwpdb.org/ <https://www.wwpdb.org/news/mmcif.wwpdb.org/>. For any further information please contact us at info@wwpdb.org. -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email:jasmine@rcsb.rutgers.edu Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 ===========================================================