1VIT

THROMBIN:HIRUDIN 51-65 COMPLEX

1VIT の概要

• エントリーDOI: 10.2210/pdb1vit/pdb
• 分子名称: EPSILON THROMBIN, ALPHA THROMBIN, HIRUDIN, ... (7 entities in total)
• 機能のキーワード: complex (serine protease-inhibitor), hydrolase, serine protease, blood coagulation, complex (serine protease-inhibitor) complex, complex (serine protease/inhibitor)
• 由来する生物種: Bos taurus (cattle); 詳細
• タンパク質・核酸の鎖数: 7
• 化学式量合計: 75350.64

構造登録者

Vitali, J.,Edwards, B.F.P. (登録日: 1996-01-31, 公開日: 1997-04-21, 最終更新日: 2024-11-13)

主引用文献

Vitali, J.,Martin, P.D.,Malkowski, M.G.,Olsen, C.M.,Johnson, P.H.,Edwards, B.F.
Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement.
Acta Crystallogr.,Sect.D, 52:453-464, 1996

PubMed Abstract: Crystals of the bovine thrombin-hirudins(51-65) complex have space group P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin molecules in the asymmetric unit. Only one thrombin molecule could be located by generalized molecular replacement; the second was fit visually as a rigid body to an improved electron-density difference map. The structure was refined to R = 0.192 with two B values per residue (main chain and side chain) at 3.2 A. The polar interactions of the peptides with the exosite of thrombin show differences consistent with the known flexibility in the interactions of the C-terminal peptide of hirudin with thrombin. The hirudin peptide in complex 2 has a higher temperature factor as compared with peptide 1 which may be correlated partly with a larger number of short-range electrostatic interactions between peptide 1 and thrombin and partly with the fact that thrombin 2 is epsilon-thrombin which is cleaved at Thr149A near the peptide binding site. Later, using this structure as a test case, it was shown that the position for the second thrombin could also be determined by a novel modification of the molecular-replacement method in which the contribution of the known molecule is subtracted from the structure factors. This approach is facile and applicable to any crystal containing two or more macromolecules in the asymmetric unit in which some but not all of the molecules can be determined by molecular replacement.

PubMed: 15299666
DOI: 10.1107/S0907444996000364

実験手法

X-RAY DIFFRACTION (3.2 Å)