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3D view of L-Cystine modification in entry PDB ID 4V1J.

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Protein Modifications in the PDB have been mapped to the RESID database of Protein Modifications and the associated Protein Modifications Ontology (PSI-MOD).  Explore these modifications with the new Protein Modification Browser, Advanced Search, and the 3D View and Sequence options on Structure Summary pages. A detailed overview is available.

Biological assembly files for large structures are now available in PDBx/mmCIF format from Structure Summary pages.   The biological assembly is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule. The PDBx/mmCIF format has no restrictions on the number of atoms and chains and can hold biological assemblies of any size.  For more information, see PDB-101’s biological assembly tutorial.   These data files can be downloaded from each Structure Summary page.

3Validation Summary Slider

In May, wwPDB Validation Reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive were publicly released. 

RCSB PDB prominently displays the Validation Summary Slider graphic at the top of all Structure Summary pages and links to the full report PDF.

wwPDB Validation Reports assess the quality of each structure and highlight specific concerns, by examining the coordinates of the atomic model derived from either NMR and 3DEM, and by comparing the coordinates of the atomic model derived from NMR with primary experimental data therefrom. Readily interpretable summary information compares the quality of the atomic model with structural models from across the entire archive, thereby helping users of PDB data critically evaluate the quality of each archival entry.

These new validation reports implement recommendations provided by NMR and 3DEM community experts on validation, while reusing elements of the validation schema developed for structures determined by X-ray crystallography.

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