The crystal structure of Bowman-Birk type protease inhibitor A-II from peanut was refined at 2.3 A resolution using a restrained least-squares method. The crystallographic R-factor is 0.196 for 7697 reflections with F > 3 sigma (F) in the range from 6.0 to 2.3 A resolution. Two molecules in an asymmetric unit are independently refined and, their structures are compared with each other. The inhibitor molecule has an elongated shape with two reactive sites, one at both ends of the longest dimension. As a secondary structure, a 4-stranded beta-sheet-like structure is found, in which two water molecules bind two 2-stranded beta-sheets together with six hydrogen bonds. The molecule is constructed by two homologous domains which are related by an intramolecular pseudo 2-fold axis. The structure and atomic B-factors of peptide loops containing a reactive site were compared with that of adzuki bean Bowman-Birk type inhibitor in the complex with bovine beta-trypsin. This comparison shows that no significant structural change occurs in the reactive site of inhibitor at the formation of the inhibitor-protease complex, but structural rigidity around the reactive site seems to increase.