Introduction - This script shows the complex between the pancreatic trypsin inhibitor (PTI) and trypsin. PTI is a small protein, Mr= 8 kDa. PTI binds to trypsin with high affinity because it contains a peptide bond that is a transition state analog. Scroll down until the text corresponding to the view is visible. (Based on 2ptc.pdb, M.Marquart et al. Acta Crystallogr., Sect. B 39 480 (1983)).
This is the complex between PTI (GREEN) and Trypsin (WHITE).
A lys (RED) of the inhibitor binds in the specificity pocket of trypsin.
The peptide bond between the lys and ala is distorted, which forces the carbonyl oxygen (GREEN) of the peptide bond into the oxyanion hole.
The peptide bond involving the lys is non planar and resembles the reaction transition state - this inhibitor is a natural transition state analog.