Protein Structure

$1,623,075ZIAFY2025CANIH

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

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Abstract

We have been investigating the quality of macromolecular structures deposited in the Protein Data Bank (PDB), as well as in derivative repositories, exemplified by PDB-REDO. We found a significant number of deposits with very significant problems in either the model of the macromolecule or of the ligands. Specifically, we found a large number of medium-to-high resolution structures of proteins with missing solvent, leading to a proposal of how many solvent molecules should be expected as a function of resolution of diffraction data. We also found a significant number of deposits that were duplicated and informed the PDB about this problem. We also analyze the quality of data in individual families of proteins, with the first example being the cAMP-dependent kinases.

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