Bovine pancreatic phospholipase A2 covalently inhibited by p-bromo-phenacyl-bromide was crystallized from 50% (v/v) 2-methyl-2,4-pentanediol. The space group was P3(1)21 with cell dimensions a = b = 46.73 A and c = 102.5 A (1 A = 0.1 nm). Diffraction data were collected by oscillation photography from one single crystal of dimensions 0.2 mm x 0.2 mm x 0.2 mm. The crystal structure was determined to a resolution of 2.5 A by crystallographic refinement of a starting model, which consisted of native bovine pancreatic phospholipase A2 positioned and oriented in the P3(1)21 cell as in the bovine pro-phospholipase A2. The crystallographic R-factor decreased from 0.378 to 0.197 after 70 refinement cycles. For the greater part the three-dimensional structure was very similar to that of native phospholipase. The inhibitor group shows up clearly. However, as in solution, there is no calcium ion bound any more in the active site, and this causes a significant conformational change in the loop from residue 59 to 73. This loop is remote from the calcium binding site. Interestingly, this is the same loop that also shows different conformations in other phospholipase A2 molecules. The inhibitor molecule has hydrophobic interactions with Phe5 and Cys45. Rational design of specific and potent inhibitors of phospholipase A2 catalysis is discussed on the basis of the present three-dimensional structure.