Dear all,
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
andMetalCoord <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
atGitHub <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 [email protected].
Kind regards,
Deborah Harrus, on behalf of the wwPDB
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
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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