Metalloproteins represent ~30% of the PDB archive. Ensuring FAIR data
practices for metalloproteins is highly impactful. wwPDB has worked
closely with metalloprotein community to collect feedback and
requirements and community software developers to adopt their tools
(FindGeo https://doi.org/10.1093/bioinformatics/bts246 from MetalPDB
and MetalCoord https://doi.org/10.1107/S2059798324011458 from CCP4) to
enhance metalloprotein annotation.
As announced in 2025
https://www.wwpdb.org/news/news?year=2025#68fbbb6b829c3fea8eaf395b,
the PDBx/mmCIF dictionary extensions, example files were 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.
All existing polyatomic metal containing PDB entries and CCDs have been
updated to make metalloprotein structures findable and reusable with
more complete chemical description and metal coordination annotation.
About ~900 metal-containing polyatomic CCDs and ~15,500 affected PDB
entries are updated and publicly available at both PDB current and Beta
archives.
In the impacted PDB entries, metal-protein interaction is provided.
Metal coordination geometry are calculated based on the coordinate model
(by FindGeo and MetalCoord) and assessed by comparing to the
regular/allowed metal coordination geometry annotated in the CCD.
Details are available at wwPDB.org.
https://www.wwpdb.org/documentation/metalloprotein-remediation
For any further information please contact us at info@wwpdb.org.
Read the full news here:
https://www.wwpdb.org/news/news?year=2026#6a847d2b3bf5580b84a87d31
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