[3dem] Remediation of Metal-containing PDB Entries and CCDs

[Justin Flatt]

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 [1] from MetalPDB and MetalCoord [2] from CCP4) to enhance 
metalloprotein annotation.

As announced in 2025 [3], the PDBx/mmCIF dictionary extensions, example 
files were provided at GitHub [4] 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.

  [5]_The electron transport chain, replete with metallocofactors (e.g., 
SF4, HEM) needed to create the electrochemical gradient that powers ATP 
synthase. New annotations on metal-protein interactions and coordination 
geometry provide context about the metal environment necessary for these 
metals to carry out their functions. _

Details are available at wwPDB.org. [5]

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

Links:
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[1] https://urldefense.com/v3/__https://doi.org/10.1093/bioinformatics/bts246__;!!Mih3wA!DzSnFC0tz94c7iQ06-llk2yHPHfLoadr0KtyTe3QE9TTP1b3LtE-klslJ39zDe_aF1Z1Ef1LUWtwdIdBE5-CVdpF$ 
[2] https://urldefense.com/v3/__https://doi.org/10.1107/S2059798324011458__;!!Mih3wA!DzSnFC0tz94c7iQ06-llk2yHPHfLoadr0KtyTe3QE9TTP1b3LtE-klslJ39zDe_aF1Z1Ef1LUWtwdIdBE0DD5CZQ$ 
[3] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2025*68fbbb6b829c3fea8eaf395b__;Iw!!Mih3wA!DzSnFC0tz94c7iQ06-llk2yHPHfLoadr0KtyTe3QE9TTP1b3LtE-klslJ39zDe_aF1Z1Ef1LUWtwdIdBE8ZMuE7h$ 
[4] https://urldefense.com/v3/__https://github.com/wwPDB/metallo-extension__;!!Mih3wA!DzSnFC0tz94c7iQ06-llk2yHPHfLoadr0KtyTe3QE9TTP1b3LtE-klslJ39zDe_aF1Z1Ef1LUWtwdIdBE-rfo7o0$ 
[5] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/metalloprotein-remediation__;!!Mih3wA!DzSnFC0tz94c7iQ06-llk2yHPHfLoadr0KtyTe3QE9TTP1b3LtE-klslJ39zDe_aF1Z1Ef1LUWtwdIdBEytlKN0R$ 
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