Introduction - This script compares the substrate-binding pockets of elastase and chymotrypsin, two seine proteases. [Based on 7est.pdb - IL DeLaSierra, E Papamichael, C Sakarelos, JL Dimicoli, T Prange J. Mol. Recog. 3, 36 (1990) and 8gch.pdb - M Harel, CT Su, F Frolow, I Silman, JL Sussman Biochemistry 30 5217 (1991)].
Elastase and chymotrypsin are both serine proteases. Note the close similarity of the tertiary structures of these enzymes.
Indeed, the structure of the catalytic triad is almost identical in the two enzymes.
Elastase has a specificity for substrates with small alipathic sidechains, which bind near the catalytic triad and are held in place by large bulky sidechains of the enzyme.
Chymotrypsin has a specificity for substrates with large aromatic sidechains, which bind near the catalytic triad and are held in place by a binding pocket whose entrance contains Gly sidechains with Ser at the bottom of the pocket.
Here we see how the large sidechain of the chymotrypsin substrate is incompatible with the elastase binding pocket.
Here we compare the binding of the chymotrypsin substrate to chymotrypsin and elastase.
Here we compasre the binding of the elastase substrate to chymotrypsin and elastase.