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Correcting cis‐trans‐transgressions in macromolecular structure models
Author(s) -
Waibl Franz,
Liedl Klaus R.,
Rupp Bernhard
Publication year - 2022
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/febs.15884
Subject(s) - moiety , molecule , identifier , identification (biology) , simple (philosophy) , macromolecule , chemistry , protein data bank (rcsb pdb) , computer science , stereochemistry , biology , programming language , philosophy , biochemistry , organic chemistry , botany , epistemology
Many macromolecular X‐ray and cryo‐EM structure models deposited in the PDB contain biologically relevant small molecule ligands with unsaturated fatty acid acyl chains, whose cis‐trans stereochemistry is incorrect. The molecules are either not properly defined in their stereochemical restraint files, or the proper stereochemistry is neglected during model building. Often, the same molecules appear in deposited models in both isomeric configurations, one of which is almost always incorrect, and the use of the same moiety (HET) identifier and restraint files in model refinement is wrong. We present case studies of frequently occurring molecules and a compilation of identified cases of C‐C=C‐C cis‐trans geometry in the deposited structure models. Full listings of cis/trans torsion angles are provided for models with commonly occurring molecules to assist identification and correction of cis‐trans errors and prevent inadvertent use of incorrect models. Caveats for users, advice for modellers and suggestions for remediation efforts with a simple but effective restraint file modification are provided.