Practice exercise

Citrate synthase complexed with ligands

Load the PDB file with code 6CSC, but only one chain (monomeric enzyme):

• sample file 6csc_monomer.pdb (right-click and choose download or save as)
• command in the console: load =6csc filter "*:A";

Using the mouse, find out the name of the ligands present; write those names down.

If it does not look like the image on the right, adjust the rendering:

• select all; spacefill 23%; wireframe 0.15;
  (or popup menu > Style > Scheme > Ball and stick)
• select protein; cartoon only;
  (or popup menu > Select > Protein > All then > Style > Scheme > Ball and stick)
• select all;

Activate highlight for working more easy:

• pop-up menu > Select > Selection halos
• menu > Select > None

Now let's have a look at the citrate pocket:

In the console, type:

• select within(3.0, CIT); // see what got selected
• define ligandsite selected; // defining a "named atom set" allows to reuse later
• menu > Style > Scheme > Ball and stick
• maybe: display ligandsite; // hides everything else
  then: display all;

Try result setting other distances.

Better:

• select within(3.0, CIT) and not CIT; .
• define ligandsite selected;

How to measure distances:

• with the mouse: double-click on first atom, move to target atom, double-click to fix the measurement
• with a command: measure (atom1) (atom2); // learn how to specify atoms
• you can get a listing from the toolbar button