Part 1. Visualisation of protein molecules and ligand interactions.
Extracting the liganda)Download pdb file “6lze”(from www.pdb.org)and open it in PyMOL.
There are very clear instructions on how to install PyMOL, open files and manipulate the viewin the “modellingmanual” available fromthe practical E Moodle page(Reference 1, Chapter 4).
It is highly recommended that you work your waythrough the whole of chapter 4 before continuing.
b)Determine key polar interactions between the ligand and the active site, and measure the distances.
In PyMOLgo to the tab ‘all’ –> click ‘A’ (it will show you a drop-down menu) –> ‘preset’ –> ‘ligand sites’ –> ‘cartoon’Take a screen shot of the active site and add to your pre-lab submission sheet (see template providedon Moodle).
In this representation of the active site the close polar contacts are highlighted (by dashes lines).
By selecting “Show” then “labels” the distances will be added to the view. Alternatively, select’Wizard’from the main menu, then–> ‘Measurement’.–>“distances”.
Select two atoms from both the protein and the ligand(that are in contact e.g. via an H-bond).
Repeat for all close polar contacts.Tabulate the dataand add to the pre-lab template.e.g.
Protein residue contact distance/ AAsn XYZ ligand C=O2.4etc…(see template for further details)Note: that some polar contacts are between the ligand and the peptide backbone.
To see the backbone amide groups more clearly select “H”(for “hide”)and “cartoon” (from the dropdown menu).The amide backbone should now be visible.Ignore any polar contacts to water molecules.
c)Extract the ligand from the complex (see video) and create 2 new files. One containingonly the ligand, and the other containing onlythe protein.
Name the files: protein.pdbandligand.pdbTake screen shots of boththese molecules and add to the pre-lab template.It is important that you keepthese files (and files created subsequently)in the same folder.
