C3: Trypsin (Serine Protease)

Trypsin is a digestive enzyme that is a member of a large class of enzymes that utilize a Ser residue to cleave esters as well as peptide bonds. Other examples of Serine proteases include chymotrypsin as well as elastase. The peptide backbone is shown in the Jmol window on the left.

The Scale of Things: How large is Trypsin? To find out do the following:
Measurement ¬ Click for distance measurement

Secondary Structure: Is Trypsin largely helix or sheet? To find out try the following:
Color ¬ Atoms ¬ By scheme ¬ Secondary Structure
Helicies are red, sheets are yellow. Is myoglobin composed of mainly sheet or helix? Is Trypsin composed of mainly sheet or helix?

Catalytic Triad: Serine proteases have three residues that are critical for catalysis. These are a Ser195, His57, and Asp102 residue. It is difficult to select individual residues for display with the Jmol menu (however, this is easy using the console. We will do both.

Using the Menu: Select ¬ Protein ¬ By residue name ¬ Ser
Style ¬ Scheme ¬ Ball and Stick
Select ¬ Protein ¬ By residue name ¬ His
Style ¬ Scheme ¬ Ball and Stick
Select ¬ Protein ¬ By residue name ¬ Asp
Style ¬ Scheme ¬ Ball and Stick
The problem with the above method is that all His, Ser, and Asp residues are displayed!

Using the Console:
Select ¬ Console
Now type the following into the lower part of the console box:

You can add the bound inhibitor by typing the following in the console:
  • select *:B
  • wireframe 0.3