Abstract

The structure of thrombin protein Oncorhynchus mykiss had not yet been resolved by NMR or X-ray diffraction method. In the present work, we have modeled the structure of protein using Modeller 9v1, taking human thrombin protein as the template. Furthermore, the antithrombin protein was docked with the best model generated by R-dock and Z-dock module of INSIGHT II and the nine potential amino acids involved in anchoring of antithrombin with thrombin were identified as: Leu3, Trp27, Asn120, Glu123, Pro133, Ile148, Ser152, Gly204 and Phe215, respectively. The study also showed surface complimentarily between O. mykiss thrombin and antithrombin which can be helpful for designing new antithrombin molecules for the treatment of blood clotting disorders in humans.

Key words: Antithrombin protein, homology modeling, r-dock, thrombin, z-dock.