Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

IP
Irina Persikova
Tue, Oct 28, 2025 6:38 PM

Metalloproteins represent ~30% of the PDB archive. Ensuring FAIR data
practices for metalloproteins is highly impactful. wwPDB will update
existing polyatomic metal containing PDB entries and CCDs to make
metalloprotein structures findable and reusable with more complete
chemical description and metal coordination annotation. About ~900
metal-containing polyatomic CCDs and ~13000 affected PDB entries will be
updated and publicly available in Q3 2026.

The updates include standardization of calculated charge, improved ideal
coordinate calculation, metal coordination and pi bond annotation, and
coordination geometry annotation in the CCDs and impacted PDB entries.
This remediation effort includes adoption of metalloprotein community
software (FindGeo from MetalPDB and MetalCoord from CCP4).

Details are available at wwPDB.org.
https://www.wwpdb.org/documentation/metalloprotein-remediation

The PDBx/mmCIF dictionary extensions, examples of PDBx/mmCIF files of
remediated data representing various cases, and the corresponding
proposed Chemical Component Dictionary definitions are provided at
GitHub https://github.com/wwPDB/metallo-extension for testing and
adoption by key stakeholders during the development stage, including the
metalloprotein community, refinement software developers,
cheminformaticians, and 3D visualization software.

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

Full news:
https://www.wwpdb.org/news/news?year=2025#68fbbb6b829c3fea8eaf395b

On behalf of the wwPDB

--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
mailto:irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu http://iqb.rutgers.edu |
facebook https://www.facebook.com/RCSBPDB | twitter
https://twitter.com/buildmodels

Metalloproteins represent ~30% of the PDB archive. Ensuring FAIR data practices for metalloproteins is highly impactful. wwPDB will update existing polyatomic metal containing PDB entries and CCDs to make metalloprotein structures findable and reusable with more complete chemical description and metal coordination annotation. About ~900 metal-containing polyatomic CCDs and ~13000 affected PDB entries will be updated and publicly available in Q3 2026. The updates include standardization of calculated charge, improved ideal coordinate calculation, metal coordination and pi bond annotation, and coordination geometry annotation in the CCDs and impacted PDB entries. This remediation effort includes adoption of metalloprotein community software (FindGeo from MetalPDB and MetalCoord from CCP4). Details are available at wwPDB.org. <https://www.wwpdb.org/documentation/metalloprotein-remediation> The PDBx/mmCIF dictionary extensions, examples of PDBx/mmCIF files of remediated data representing various cases, and the corresponding proposed Chemical Component Dictionary definitions are provided at GitHub <https://github.com/wwPDB/metallo-extension> for testing and adoption by key stakeholders during the development stage, including the metalloprotein community, refinement software developers, cheminformaticians, and 3D visualization software. For any further information please contact us at info@wwpdb.org. Full news: https://www.wwpdb.org/news/news?year=2025#68fbbb6b829c3fea8eaf395b On behalf of the wwPDB -- IRINA PERSIKOVA, Ph.D. Deputy Biocuration Lead, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4938 | E: irina.persikova@rcsb.org <mailto:irina.persikova@rcsb.org> rcsb.org <www.rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels>