The Scale of Things: How large is Trypsin? To find out do the
following:
Select¬Mouse Click Action¬Toggle Distance Monitor
Now use the
right mouse button to click on two atoms to find the distance between them.
After you are done you probably want to reload the page by clicking in the
left frame.
Secondary Structure: Is Trypsin largely helix or sheet? To find out try the following:
Select¬Protein¬Sheet
Select¬Change Color To¬Yellow
Did anything change color? Now try this:
Select¬Protein¬Helix
Select¬Change Color To¬Yellow
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 Chime (however, this
is easy for RasMol). You can try the following to get some idea of where
these three residues are located:
Select¬Residue¬ASP
Display¬Ball & Stick
Select¬Residue¬HIS
Display¬Ball & Stick
Select¬Residue¬SER
Display¬Ball & Stick
You should now see ALL of the Asp, Ser, and His residues displayed! It is
difficult to identify the three which belong to the triad. It might be
helpful to display an inhibitor and color it yellow:
Select¬Chain¬B
Display¬Ball & Stick
Select¬Change Color To¬Yellow
The catalytic triad can be more clearly seen by pressing the following button: