Display the molecule within PyMOL and use the Preset>Pretty mode to create a ribbon diagram. Colour this by chain. At this stage you may just see the bound ligand as a tiny molecule - one bound to each polypeptide chain.
Now select the Display menu at the top of the page and select the sequence option. This will display the sequences of the polypeptide chains and the bound ligands above the display of the structure. Once this is done, it is possible to use this to select individual residues or ligands and modify the way they are displayed.
Scroll along the sequence display until you see the code for the ligand. It should be at the end of the sequence for the first polypeptide chain. It will also appear at the end of the sequence for the second polypeptide chain, but you need only change the display for the ligand bound to one protein chain. Click on the name for the ligand. This selects all the atoms in the ligand. Now you can change the display of this selection (referred to by (sele) in the menu at the right hand side. You could for example show it as spheres and give it a particular colour
Once you have changed the display for the ligand, click on it once again to deactivate this selection. We can apply the same process to highlight the individual amino acid residues which are involved in the active site. Select each of the amino acids you found when answering question 6 and highlight them e.g. by displaying as ball and stick and giving particular colours.
The amino acids highlighted should be close to the ligand you have displayed.
Now you know how to create a picture of a molecule indicating ligands bound and highlighting specific amino acids. This protein is an enzyme called Triose Phosphate Isomerase and its structure is one of the superfolds we encountered in lecture 3. Many enzymes with different functions have the ame fold, consisting of a barrel of parallel beta strands surrounded by alpha helices. In terms of supersecondary structures this is made up of consecutive beta-alpha-beta motifs. Usually the substrate binds to the inside of the beta barrel, at the C-terminal end of the strands. You should be able to see this for this example - the ligand is close to the pointed end of the beta strand arrows.
Save an image of this protein and its ligand binding residues and include it as part of your assignment.