04.3 Looking at the Active Site

4.3 Looking at the Active Site

The easiest way to select specific residues is to look at the sequence of your protein and select the amino acids you want by their one letter code. If you know which amino acids make up the active site, you can select them in this way to make an active site selection. Click display, then click sequence. You will see a new line appear at the top of the display window (it will be in the same colour as your protein).

From here you can now select individual residues (by clicking on their letter in the sequence) and create new selections. Rename your selection in the same way as before and choose a colour for these residues to make them stand out from the rest of the protein. (Note – crystal structures don’t always contain the entire sequence so you may find that your first residue is not numbered 1.)

Here we have selected some of the active site residues of this protein, G143, S144, C145, H163 and E166 and shown them as sticks (click the show button, then click sticks), colouring them yellow and by element. You can make your new selection the centre of your protein by selecting the action button, then clicking centre. You can also label these residues by clicking on the label button, and then clicking residues (to display the three letter code, or click residues (one letter) to display the one letter code labels).

This is an easy way to build up a colour coded picture of your active site, by selecting all the active site residues, and then colour coding them based on their function (for example, cyan for oxyanion hole, or orange for hydrophobic pocket etc.) you can build a ready-made active site pdb file. Having this pre-made file available can help you to easily view your docking results in your target protein, and colour coding it allows you to easily orientate yourself when viewing many different ligands.

Above is an example of a colour coded active site file with some docking results shown. Here the protein was coloured white (not by element, to create an entirely white surface), then the individual residues of the active site were selected and colour coded (again not by element, to give solid colours). You can see the colour coding also shows up on the sequence, which can help you easily find the residues you are looking for once you’ve colour coded them.

Below is another example of a pre-made file with docking results also opened. Here the residues were colour coded by element (as this is the best way when viewing their stick form) and they were labelled with the three-letter code. The docking results were also coloured to distinguish easily between the active site residues and the docked ligands. Note here that only the active site residues of the protein are shown, the rest of the proteins structure is hidden.

In addition to colouring specific active site residues, you can use the sequence to easily select certain elements of the proteins structure. For example, to colour one helix differently to the others, you can select the point on the cartoon structure where the helix begins, and the point where it ends, and then scroll along the sequence to find which residues you highlighted. You can then select all the residues between these two and easily highlight the whole helix. After renaming the selection and choosing a colour you will have something looking like this:

If you wanted to centre and zoom in on this secondary structure element and view the residues you can click on the show button of the helix selection, and then click sticks. The carbon backbone and side chains of all the residues making up the helix will now be visible.

You could hide the rest of the protein in a similar way by selecting the rest of the sequence, naming the selection, and then clicking hide everything, to leave just this helix showing in the display window. Alternatively, you could hide the entire protein by clicking hide, then everything on the protein entry (6YB7 on the side menu), and then show the helix again by clicking show, then cartoon (on the helix entry), and then again click show, and then sticks.