Dear all,
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 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.
For any further information please contact us [email protected].
Read this news online:
https://www.wwpdb.org/news/news?year=2025#68fbbb6b829c3fea8eaf395b
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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