CRYSTAL-STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND P-AMIDINOPHENYLPYRUVATE AT 1.6 ANGSTROM RESOLUTION

Crystals of human alpha-thrombin complexed with hirugen and the alpha- keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffr act to 1.6 Angstrom resolution were obtained by soaking an alpha-throm bin-hirugen crystal in a solution of APPA. The crystal structure was d etermined using the difference Fourier method and refined to an R fact or of 18.7% at 1.6 Angstrom resolution. This structure is the highest resolution structure of the thrombin molecule that is currently availa ble. With the exception of the region near Arg77A-Asn78, the structure s of the thrombin and hirugen molecules in the ternary complex are sim ilar to those reported for the thrombin-hirugen binary complex. As pre viously determined for the APPA-trypsin complex, the carbonyl carbon a tom of APPA forms a covalent bond with O gamma of Ser195 of thrombin t o yield a ''transition-state'' analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombi n and trypsin reveals differences in hydrogen bonding and shows for th e first time that the S1 site of thrombin is larger than that of tryps in and as a result thrombin may be able to accommodate a bulkier P1 gr oup than trypsin. (C) 1995 Academic Press, Inc.