The Scale of Things: How large is Trypsin? To find out do the
following: Secondary Structure: Is Trypsin largely helix or sheet? To find out try the following: 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 Using the Console:
Measurement ¬ Click for distance measurement
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?
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!
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: