The substrate-like ‘canonical' inhibition by the ‘small’ serine proteinase inhibitors and the product-like inhibition by the carboxypeptidase inhibitor have provided the only atomic models of protein inhibitor–proteinase interactions for about 15 years. The recently published structures of cystatin/stefin – papain complexes and of hirudin – thrombin complexes reveal novel non-substrate - like interactions. In addition, the structure of pro-carboxypeptidase showes a mode of inactivation which bears resemblance to proteinase/protein inhibitor systems. Considerable progress in understanding the transition between native and cleaved states of the serpins has also been made by several recent structural studies.
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P1, P2, P3 etc. and P1′, P2′, P3′ etc., designate substrate/inhibitor residues amino-terminal and carboxy-terminal of the scissile peptide bond, respectively, and S1, S2, S3 etc. and S1′, S2′, S3′ etc., the corresponding subsites of the cognate proteinases . Abbreviations of the inhibitors are explained in Table 1