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2023 Deposition Statistics

In 2023, 17,063 experimentally-determined structures were deposited to the PDB archive.  Data were processed by wwPDB partners RCSB PDB, PDBe, PDBj and PDBc.

Of the structures deposited in 2023, 83.9% were deposited with a release status of hold until publication  8.1% were released as soon as annotation of the entry was complete  and 8.0% were held until a particular date. 59.8% of these entries were determined by X-ray crystallographic methods  2.0% were determined by NMR methods  and 38.0% by 3DEM.

7,770 EMDB maps were released in the archive.

14,488 new PDB structures were released in 2023, accounting for 6.8% of the year-end total holdings of  214,121 available entries.

1,053 SARS-CoV-2 structures were released, for a total of 3,914 available at the start of the new year.


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

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.  Details at wwPDB.org.

Backbone Annotation and Standardization of Peptide Residues

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wwPDB has rolled out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs have been updated accordingly. This improves the Findability and Interoperability of the PDB data and opens up new opportunities to use the updated peptide residue annotation.

The atom nomenclature of peptide backbone atoms in CCD files has been standardized  to ensure carboxyl groups, amino groups and side chain linked carbons (C-alpha) follow a standard atom nomenclature. This allows clear identification of backbone atoms for peptide residues across the whole archive.

 

Coming in 2024: Deprecation of FTP File Download Protocol in the PDB Archive

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Given that the majority of file download activity on the internet has moved to HTTP/S, wwPDB plans to deprecate FTP download protocol on November 1, 2024.

Support for the RSYNC protocol, which offers additional functionality, will continue to be maintained. As announced previously, wwPDB supports protocol-specific DNS names:

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