[3dem] Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

[Justin Flatt]

Dear All,

  [1]_Metal-protein interaction annotation and metal coordination 
annotation and assessment_

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. [1]

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 [2] 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 at wwpdb.org.

Best wishes,
Justin Flatt on behalf of the wwPDB

Links:
------
[1] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/metalloprotein-remediation__;!!Mih3wA!AftFyuv2mUFAFn0uUdffRAu84_Y6NM5vqa75kGigMd8nIX5c3oWSUPtlyHEpTbUt2R5MPJ4ti81OL8WECZvysIOV$ 
[2] https://urldefense.com/v3/__https://github.com/wwPDB/metallo-extension__;!!Mih3wA!AftFyuv2mUFAFn0uUdffRAu84_Y6NM5vqa75kGigMd8nIX5c3oWSUPtlyHEpTbUt2R5MPJ4ti81OL8WECYeYcF-h$ 
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