3VXF
X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5
Summary for 3VXF
| Entry DOI | 10.2210/pdb3vxf/pdb |
| Related | 3VXE |
| Related PRD ID | PRD_001145 PRD_001148 |
| Descriptor | Thrombin light chain, Thrombin heavy chain, BIVALIRUDIN, ... (6 entities in total) |
| Functional Keywords | serine protease, hydrolysis, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 4 |
| Total formula weight | 36297.27 |
| Authors | Yamada, T.,Kurihara, K.,Masumi, K.,Tamada, T.,Tomoyori, K.,Ohnishi, Y.,Tanaka, I.,Kuroki, R.,Niimura, N. (deposition date: 2012-09-12, release date: 2013-09-04, Last modification date: 2020-07-29) |
| Primary citation | Yamada, T.,Kurihara, K.,Ohnishi, Y.,Tamada, T.,Tomoyori, K.,Masumi, K.,Tanaka, I.,Kuroki, R.,Niimura, N. Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta, 1834:1532-1538, 2013 Cited by PubMed Abstract: 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. PubMed: 23712263DOI: 10.1016/j.bbapap.2013.05.014 PDB entries with the same primary citation |
| Experimental method | NEUTRON DIFFRACTION (2.752 Å) X-RAY DIFFRACTION (1.602 Å) |
Structure validation
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