Introduction - This script shows some aspects of the mechanism of the serine protease chymotrypsin. Scroll down until the text corresponding to the view is visible. (Based on 8gch.pdb, M.Harel et al. Biochem. 30 5217 (1991) and 2tbs.pdb, A.O.Smalas Proteins 20 149 (1994)).
The catalytic triad is composed of His 57 (RED), Asp 102 (BLUE) and Ser 195 (GREEN).
Note how proton (YELLOW) transfer is setup by the arrangement of the triad.
Here is a substrate analog (MAGENTA) bound in the active and the residues in the protein that interact with it
Substrate binding involves two interactions: (1) the specificity pocket, which binds a Trp is shown in GREEN, and (2) nonspecific binding of the poylpeptide chain via hydrogen bonds shown in YELLOW.
Here we see the catalytic traid (BLUE) poised to attack the substrate.
Here we see that the tetrahedral intermediate is stablized by hydrogen bonds between the oxygen (CYAN)
of the tetrahedral intermediate and the peptide backbone of the oxyanion hole (ORANGE).
In trypsin, the specificity pocket has a negatively charged Asp that binds to the basic sidechains Lys or Arg. In this view an inhibitor, benzamidine is bound to the active site.