During replication of hepatitis Cvirus (Hev), the final steps of polyprotein processing are performed by a viral protease located in the N-terminal one-third of nonstructural 3 (NS3). The structure of NS3 protease domain composed of 1-189 amino acids from Hov BK strain was solved by X-ray crystallography at 2.4 Å resolution. The protein folds as a typical trypsin-like serine protease. Its S1 pocket is shallow and nonpolar, and is formed by the side chains of invariant residues Leu-135, Phe-154 and Ala-157 primarily. The architecture of S I pocket can accommodate the side-chain of Thr or Cys residue at P1 position of substrate. Zinc binding site, which composes of the side-chains of Cys-97, -99, -145 and His-149, is found to contribute the stabilization of protein folding.