Now you have downloaded the coordinates you can view them using Rasmol (official documentation, and an older, local manual). You can start Rasmol by going to a Unix window (make sure you are in the right directory or at least know where the PDB file is), and type rasmol. Then load the coordinates by typing load pdb <filename> (or use "Open" from the "File" menu). If the bonds are not already displayed, select "Wireframe" from the "Display" menu.

If you are not familiar with Rasmol, spend some time to read the manual, and to rotate, translate and zoom the structure (see the table below), and experiment with the items in the "Display" and "Colours" menus.

Operation Action
Left mouse button Rotate x-y
Right mouse button Translate x-y
Shift-key + left mouse button Zoom in/out
Shift-key + right mouse button Rotate z
Control-key + left mouse button Slab plane

Select "Cartoons" from the "Display" menu, and "Group" from the "Colours" menu.

Q. 12. How many alpha-helices and how many beta-strands does the structure contain ? Would you classify this structure as "mainly alpha", "mainly beta", or "alpha+beta" ?

The active site, as in all serine proteases, contains the catalytic triad Asp-His-Ser. This is located in a cleft in subtilisin. Try and identify these residues in subtilisin by looking at the structure. First, try to locate the cleft; then look for a histidine residue, and see if there are an aspartate and a serine nearby.

Q. 13. What are the residue numbers of the Asp, His and Ser ?

Don't panic if you cannot find the triad (we'll find it later !) - but have a try anyhow ! It is probably easiest to select the "CPK" colour scheme (carbon atoms are white, oxygens red, nitrogens blue, sulfurs yellow) and the "Wireframe" display. You could also draw all Asp, His and Ser residues with thicker bonds once you have the wireframe display by typing "select asp,his,ser" and then selecting "Sticks" from the "Display" menu.




Practical "Structural Databases" - EMBO Bioinformatics Course - Uppsala 1999/2001 - Gerard Kleywegt

Latest update at 28 January, 2002.