3VXF

X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

3VXF の概要

• エントリーDOI: 10.2210/pdb3vxf/pdb
• 関連するPDBエントリー: 3VXE
• 関連するBIRD辞書のPRD_ID: PRD_001145 PRD_001148
• 分子名称: Thrombin light chain, Thrombin heavy chain, BIVALIRUDIN, ... (6 entities in total)
• 機能のキーワード: serine protease, hydrolysis, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 36297.27

構造登録者

Yamada, T.,Kurihara, K.,Masumi, K.,Tamada, T.,Tomoyori, K.,Ohnishi, Y.,Tanaka, I.,Kuroki, R.,Niimura, N. (登録日: 2012-09-12, 公開日: 2013-09-04, 最終更新日: 2024-11-20)

主引用文献

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

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: 23712263
DOI: 10.1016/j.bbapap.2013.05.014

実験手法

NEUTRON DIFFRACTION (2.752 Å)
X-RAY DIFFRACTION (1.602 Å)