Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

10/30

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.

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 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@wwpdb.org.

News Index

• 10/30 Coming Soon: Remediation of Metalloprotein-containing PDB Entries and CCDs

• 10/28 Watch Molecules in Motion

• 10/21 Explore Green Fluorescent Protein

• 10/19 Happy Birthday, PDB!

• 10/16 Happy Birthday, Irving Geis

• 10/14 PDB-101 Focus: Peak Performance

• 10/08 Explore Structural Biology with CSMs

• 10/07 Register for the Nov 24 Virtual Office Hour on Exploring CSMs at RCSB.org

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• 09/23 Browse Protein Structure Prediction at PDB-101

• 09/23 Register for the Sept 25 Virtual Office Hour on PDB Policies

• 09/22 wwPDB News: MolViewSpec: describe, share, and reproduce Mol* molecular scenes

• 09/16 Register Now for Webinar: Exploring Integrative Structures with RCSB.org

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• 08/26 PDB-101: Global Health

• 08/25 Register Now for Webinar: Searching the PDB for high-quality ligand-bound structures

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• 08/12 Paper Published: PDB-IHM

• 08/11 Register for the Sept 25 Virtual Office Hour on PDB Policies

• 08/05 Register for the Aug 11 Virtual Office Hour on Pairwise Alignment

• 08/05 Paper Published: rcsb-api

• 08/01 August 2 is National Coloring Book Day

• 07/29 Celebrate World RNA Day on August 1 with Eterna

• 07/29 Register Now for Webinar: Searching the PDB for high-quality ligand-bound structures

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• 07/18 Meet the RCSB PDB at ACA 75

• 07/15 wwPDB News: Transitioning to PDBx/mmCIF and Extended PDB IDs

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• 07/08 Summer Newsletter Published

• 07/03 Register for the Aug 11 Virtual Office Hour on Pairwise Alignment

• 07/01 Download New Poster: CSMs and PDB Structures

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• 06/19 Watch: Deep Dive into Computed Structure Model Exploration at RCSB.org

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• 03/27 Register Now for Crash Course: Python For Cheminformatics-Driven Molecular Docking

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• 02/25 Register for the April 7 Virtual Office Hour on Depositing IHM Data

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