PDBsum entry 3vxf

Hydrolase/hydrolase inhibitor

PDB id: 3vxf

Contents

Protein chains

28 a.a.

257 a.a.

Ligands

ASP-PHE-GLU-GLU-ILE-PRO-GLU-GLU-TYR-LEU

DPN-PRO-ARG

NAG

DOD ×158

PDB id:

3vxf

Name:

Hydrolase/hydrolase inhibitor

Title:

X/n joint refinement of human alpha-thrombin-bivalirudin complex pd5

Structure:

Thrombin light chain. Chain: l. Synonym: alpha-thrombin light chain. Thrombin heavy chain. Chain: h. Synonym: alpha-thrombin heavy chain. Bivalirudin. Chain: j. Fragment: c-terminal.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Unidentified. Organism_taxid: 32644. Other_details: enzymatically produced from bivalirudin during the crystallization. Crystallization

Resolution:

1.60Å R-factor: 0.162 R-free: 0.184

Authors:

T.Yamada,K.Kurihara,K.Masumi,T.Tamada,K.Tomoyori,Y.Ohnishi,I.Tanaka, R.Kuroki,N.Niimura

Key ref:

T.Yamada et al. (2013). 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. Biochim Biophys Acta, 1834, 1532-1538. PubMed id: 23712263 DOI: 10.1016/j.bbapap.2013.05.014

Date:

12-Sep-12 Release date: 04-Sep-13

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 257 a.a.

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

DOI no: 10.1016/j.bbapap.2013.05.014

Biochim Biophys Acta 1834:1532-1538 (2013)

PubMed id: 23712263

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.

T.Yamada, K.Kurihara, Y.Ohnishi, T.Tamada, K.Tomoyori, K.Masumi, I.Tanaka, R.Kuroki, N.Niimura.

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.