Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid
thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A
resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a
solution of APPA. The crystal structure was determined using the difference
Fourier method and refined to an R factor of 18.7% at 1.6 A resolution. This
structure is the highest resolution structure of the thrombin molecule that is
currently available. With the exception of the region near Arg77A-Asn78, the
structures of the thrombin and hirugen molecules in the ternary complex are
similar to those reported for the thrombin-hirugen binary complex. As previously
determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms
a covalent bond with O gamma of Ser195 of thrombin to yield a "transition-state"
analog of the tetrahedral intermediate. Comparison of the specificity pocket of
the APPA complexes of thrombin and trypsin reveals differences in hydrogen
bonding and shows for the first time that the S1 site of thrombin is larger than
that of trypsin and as a result thrombin may be able to accommodate a bulkier P1
group than trypsin.
