2y5a
Cytochrome c peroxidase (CCP) W191G bound to 3-aminopyridineCytochrome c peroxidase (CCP) W191G bound to 3-aminopyridine
Structural highlights
FunctionCCPR_YEAST Destroys radicals which are normally produced within the cells and which are toxic to biological systems. Publication Abstract from PubMedThe model binding site of the cytochrome c peroxidase (CCP) W191G mutant is used to investigate the structural and dynamic properties of the water network at the buried cavity using computational methods supported by crystallographic analysis. In particular, the differences of the hydration pattern between the uncomplexed state and various complexed forms are analyzed as well as the differences between five complexes of CCP W191G with structurally closely related ligands. The ability of docking programs to correctly handle the water molecules in these systems is studied in detail. It is found that fully automated prediction of water replacement or retention upon docking works well if some additional preselection is carried out but not necessarily if the entire water network in the cavity is used as input. On the other hand, molecular interaction fields for water calculated from static crystal structures and hydration density maps obtained from molecular dynamics simulations agree very well with crystallographically observed water positions. For one complex, the docking and MD results sensitively depend on the quality of the starting structure, and agreement is obtained only after redetermination of the crystal structure and refinement at higher resolution. Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site.,Cappel D, Wahlstrom R, Brenk R, Sotriffer CA J Chem Inf Model. 2011 Sep 15. PMID:21916516[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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