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

Kinases and phosphatases Pub Date : 2025-09-01 Epub Date: 2025-09-11 DOI:10.3390/kinasesphosphatases3030019
Alexander Wlodawer, Pawel Rubach, Zbigniew Dauter, Wojciech Dec, Wladek Minor, Dariusz Brzezinski, Mariusz Jaskolski
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Abstract

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.

对camp依赖性蛋白激酶晶体结构的批判性观察。
我们已经评估了PDB中所有325个沉积物的质量(截至2024年12月),这些沉积物对应(或包含)camp依赖性蛋白激酶(PKA)的催化结构域。对289种沉积的晶体结构进行了详细的分析,不仅包括原子坐标,还包括结构因素。这些结构代表了35年的研究,并不奇怪,较新的结构通常比较旧的结构质量更好。虽然发现了一些小问题,但我们没有遇到非常严重的问题。为了评估在管道和网站PDB-REDO中实施的统一的结构再细化方法是否会导致结构模型的显着改进,我们比较了最初细化的结构和PDB-REDO细化后的结构质量指标。重新改进程序仅显著改善了一些较旧的结构,而其成功通常是有限的。我们特别注意了小分子配体的质量,发现它们中的大多数都非常适合电子密度。这种类型的分析有助于在某些蛋白质家族的许多沉积物中确定最高质量的结构,因此也可以扩展到其他蛋白质组。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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