Chymotrypsin is a well-studied proteolytic enzyme that functions in our digestive tract where it assists in the hydrolysis of proteins that we eat. It readily cleaves the peptide bonds adjacent to aromatic amino acids tyrosine, phenylalanine and tryptophan. Its mechanism of action is well-understood and is often taught in undergraduate biochemistry courses as an example of the enzyme catalysis. The active site of chymotrypsin has two interesting structural features:
Your task now is to create an image that illustrates the following aspects of the chymotrypsin mechanism:
A suitable structure of chymotrypsin with a bound inhibitor in the PDB file 1AFQ. Open this file in PyMOL. It looks pretty complex, so let's simplify the view by displaying parts that are important for your assignment. Visual inspection of the PDB file reveals that the chain D is the ligand. We want to show this ligand, and the catalytic residues in some detail while displaying the rest of the protein as a surface. This is possible in PyMOL because surfaces can be set transparent, e.g. set transparency, 0.6 will make the surface 60% transparent.
Continue to the next page when you are ready to see how this can be done with PyMOL.