Introduction - This script shows the binding of a substrate analog, tosyl-L-phenylalanine chloromethyl ketone (TPCK) to chymotrypsin. In the active site, His 57 becomes covalently modified when the enzyme binds substrate analog. Scroll down until the text corresponding to the view is visible. (Based on 2gmt.pdb, K.Kreutter et al. Biochem. 33 13792 (1994)).
Here is a chloroketone substrate analog (GREEN) bound to chymotrypsin.
It makes a covalent bond to the active site His 57 (YELLOW).