To probe the covalent serpin-proteinase complex, we used wild-type and 4 new single cysteine variants (T85C, S121C, D159C, and D298C) of ␣ 1 -proteinase inhibitor Pittsburgh. Cysteines in each variant could be labeled both in native and proteinase-complexed ␣ 1 -proteinase inhibitors. Pre-reaction with 7-nitrobenz-2-oxa-1,3-diazole-chloride or fluorescein prevented complex formation only with the D298C variant. Label at Cys 121 greatly increased the stoichiometry of inhibition for thrombin and gave an emission spectrum that discriminated between native, cleaved, and proteinase-complexed serpin and between complexes with trypsin and thrombin, whereas fluorophore at residue 159 on helix F was almost insensitive to complex formation. Fluorescence resonance energy transfer measurements for covalent and non-covalent complexes were consistent with a location of the proteinase at the end of the serpin distal from the original location of the reactive center loop. Taken together, these findings are consistent with a serpin-proteinase complex in which the reactive center loop is fully inserted into -sheet A, and the proteinase is at the far end of the serpin from its initial site of docking with the reactive center loop close to, but not obscuring, residue 121.Serpins are a family of widely distributed, structurally homologous proteins (1), many of which are inhibitors of serine proteinases (2). Whereas the many other families of protein inhibitors of serine proteinases, such as the Bowman-Birk, Kazal, and Kunitz families, inhibit target proteinases by forming tight non-covalent 1:1 complexes in which neither the proteinase nor the inhibitor undergoes significant structural change in most cases (3), serpins differ not only by apparently forming covalent 1:1 acyl enzyme complexes with their target proteinases (4), but by undergoing a major conformational change during, and as an essential part of, the inhibition process (5). Because of the requirement for conformational change as part of the inhibition mechanism, knowledge of the structure of the serpin-proteinase complex is critical for an understanding of how serpins inhibit their target proteinases through kinetic trapping of a normal covalent acyl enzyme intermediate on the proteinase substrate cleavage pathway.A previous proposal that a major movement of the proteinase occurs following cleavage of the scissile bond (6) has been supported by two recent studies (7,8). In one study (8) chemical cross-linking between the proteinase and the serpin in the complex, together with a measurement of the separation between P3 and P1Ј residues of the serpin in the complex by fluorescence resonance energy transfer, was consistent with a location of the proteinase half-way down the flank of the serpin (Fig. 1) and in contact with helix F. The other study (7), from this laboratory, used fluorescence resonance energy transfer between fluorophores on the serpin ␣ 1 -proteinase inhibitor (␣ 1 PI) 1 Pittsburgh and the proteinase to compare the interfluorophore separation in the normal ...