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PDBsum entry 3vxf
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Hydrolase/hydrolase inhibitor
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PDB id
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3vxf
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References listed in PDB file
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Key reference
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Title
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Neutron and X-Ray crystallographic analysis of the human α-Thrombin-Bivalirudin complex at pd 5.0: protonation states and hydration structure of the enzyme-Product complex.
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Authors
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T.Yamada,
K.Kurihara,
Y.Ohnishi,
T.Tamada,
K.Tomoyori,
K.Masumi,
I.Tanaka,
R.Kuroki,
N.Niimura.
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Ref.
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Biochim Biophys Acta, 2013,
1834,
1532-1538.
[DOI no: ]
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PubMed id
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Abstract
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The protonation states and hydration structures of the α-thrombin-bivalirudin
complex were studied by joint XN refinement of the single crystal X-ray and
neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The
atomic distances were estimated by carrying out X-ray crystallographic analysis
at 1.25Å resolution. The complex represents a model of the enzyme-product (EP)
complex of α-thrombin. The neutron scattering length maps around the active
site suggest that the side chain of H57/H was deuterated. The joint XN
refinement showed that occupancies for Dδ1 and Dε2 of H57/H were 1.0 and 0.7,
respectively. However, no significant neutron scattering length density was
observed around the hydroxyl oxygen Oγ of S195/H, which was close to the
carboxylic carbon atom of dFPR-COOH. These observations suggest that the Oγ
atom of S195/H is deprotonated and maintains its nucleophilicity in the EP
complex. In addition to the active site, the hydration structures of the S1
subsite and the Exosite I, which are involved in the recognition of bivalirudin,
are presented.
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