A Critical Look at the Crystal Structures of cAMP-Dependent Protein Kinases

We have evaluated the quality of all 325 deposits in the PDB (as of December 2024) that correspond to (or contain) the catalytic domain of cAMP-dependent protein kinases (PKA). Detailed analysis was possible for 289 deposits of crystal structures that included not only the atomic coordinates but also structure factors. These structures represent 35 years of studies, and it is not surprising that the more recent structures are generally of better quality than the older ones. We did not encounter deposits with very severe problems, although some minor problems were found. To assess whether a uniform method of structure re-refinement, as implemented in the pipeline and website PDB-REDO, leads to significant improvement of structural models, we compared structure quality indicators for the originally refined structures and their counterparts resulting from PDB-REDO refinement. The re-refinement procedure significantly improved only some older structures, while its success was generally limited. We paid particular attention to the quality of small-molecule ligands, finding that most of them fit the electron density very well. This type of analysis helps identify the highest quality structures among many deposits for certain protein families and, thus, could be extended to other groups of proteins as well.