Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 35 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 27000 sequences, 95 000 peptide chains, and 500 000 cysteines (700 000 structural conformers); there are over 300 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide.

Cys. sqlite: Structured-information approach to the comprehensive analysis of cysteine disulfide bonds in the protein databank

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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