04.2 Viewing your Target Protein

4.2 Viewing your Target Protein

Once you have a target selected you will need to find a pdb file of it from either the Protein Data Bank website (PDB, https://www.rcsb.org/) or from your own source. Once you have this pdb file you can open it in PyMOL either from your computer as you would open any other file, or you can use PyMOL’s “fetch” function which can be used to open files directly from the PDB. Type in the command as shown below and then press enter. The command line is case sensitive so be sure to type the command correctly. Here the 6YB7 is the code name of the pdb file for the SARS-CoV-2 Main Protease, which will be used in this example. For your own protein simply replace this code with your proteins code name from the PDB.

Now you have your protein displayed in the PyMOL viewer you can interact with it and visualise it in different ways using PyMOL’s tools. You will see PyMOL has the file displayed in the side menu, clicking on the entry will make the protein disappear from view, if you have multiple files open then you can choose which files are displayed at the same time in this way. Next to the files name you can see 5 buttons which will allow you to manipulate the protein to alter the way it is shown, clicking these buttons take you to their individual menus, A = action, S = show, H = hide, L = label and C = colour.

The first thing you can try is to remove the rather ugly looking red crosses, these are the water molecules from the crystal structure and are currently being displayed as these red crosses (really these crosses are just the oxygen atoms since you cannot usually detect hydrogen atoms in crystal structures without further optimisation, see later). Click on the action menu and then click remove waters.

Alternatively, you can type the command “hide nonbonded” and then press enter. This will also remove the nonbonded water molecules from view.

Next you may want to remove all of the solvent molecules still in view, X-ray structures often contain co-solvents or other molecules to aid crystallisation. To remove these, you can select them in the display window by clicking on them all individually (they will become highlighted when you do so). You will see your selection will now show in the side menu as a (sele) entry. You can rename this selection if you wish to keep it as an entry, by clicking on the action button, and then clicking rename. Type in the new name of your selection and press enter.

You can then hide these solvent molecules by clicking on the hide button, and then clicking everything (make sure you do this on your new selection entry on the side menu and not on your whole protein entry).

Those of you who are familiar with protein structure will be able to recognise the various secondary structure elements of your protein. In this example we can see some α-helices and some β-barrel structures. PyMOL allows you to select individual amino acid residues and colour them however you like, however a quick and easy way to show the individual domains of a protein is to use the chainbows colour option. To do this, click on the colour button, then click by chain, then click chainbows. You should see something looking like the image below.

Now we can see secondary structure elements more clearly, with the three domains of this protein showing as blue, green and orange/yellow sections of the structure. You can colour your whole protein in any shade you like by using the colour menu, you can also colour specific parts of the structure by selecting them (as shown earlier for the solvent molecules) and renaming them. Simply click on the colour menu and select the colour you want. Colouring by element is a good way to easily identify individual atoms if you have any residues shown (see later), as this option will keep the oxygens red and the nitrogens blue regardless of what colour you choose your carbon sticks to be.

Currently your protein is displayed as a cartoon structure (however different files may open in different forms). To change the way your protein is displayed, click on the show button, then click whichever way you wish to display the protein, for example clicking sticks will give you this view:

Notice that the cartoon structure did not disappear when you did this, the sticks simply show as well as the cartoon. If you want to undo or hide something, click on the hide button and select the thing you wish to hide, for example to return the protein to only show its cartoon structure you can click on hide, and then sticks.

You should play around with the different ways to view your protein, including looking at the surface view of the protein (show surface) as this will show you clearly where the ligand pockets are including the active site. In this example the active site pocket is located between the two β-barrel domains, and can be easily found by noticing the yellow sulphur belonging to this proteins nucleophilic cysteine residue (cysteine protease). For the image below we have rotated the protein to give the best view (simply click and drag on the display area to move the protein and rotate the view). We have then clicked show, and then clicked surface. Note that the sulphur atom was only distinguishable in this way because we had previously coloured the protein by element.