What else can PyMOL do in addition to observing protein structure? Here I would like to use an example to illustrate how PyMOL can be used to observe the interaction between a protein and a ligand:
1, find the protein file you want
The file format that Pymol can open by default is the PDB format that everyone is familiar with. We can download it from the pdb website. Take the example of this object - 3ODU (a G-protein coupled receptor involved in cancer metastasis and HIV infection), we can directly open it by following the path below: Select File-Get PDB in the External GUI, The following dialog box appears, enter the PDB number of the protein we are looking for, click Download, you can directly download the corresponding PDB file, which is fast and convenient.
2. Operate the five buttons in the Internal GUI
All refers to all objects, 3ODU refers to the file just opened, and (sele) refers to the selected object button.
A: represents various actions on this object;
S: display a certain style of this object;
H: hide a certain style;
L: display some kind of label;
C: The color of the display.
Here is the operation process:
Click on H in all, select everything, hide all;
Click on S in 3ODU, select cartoon, and display the protein in the form of cartoon;
Click C in 3ODU, select by ss, assign color in the secondary structure, and select.
Click the S in the lower right corner.
The protein amino acid sequence appears above the window, and the small molecule inhibitor ligand ITD at position 1164 is found. Click to select.
At this point, sele will contain the residue position corresponding to the ITD. Click on the sele line A and select rename selection. The window appears.
Change sele to ITD, then click on the (ITD) line of S to select sticks, click on C, select by element, and select.
Adjust the window to make this molecule clear.
3. Find hydrogen bonds that interact with proteins and proteins.
Click on the ITD line to select find, select polar contacts, and then select as needed, here to select other atoms inobject, several yellow dashed lines appear in the molecular display window.
A new line appears below the ITD line.
This is the object of the hydrogen bond. Click on the C in the row, select red and display the hydrogen button as red.
4. Displaying residues that form hydrogen bonds with ITD
Click on the S of the 3ODU row, select lines, display the side chains of all residues, use the mouse to rotate the protein to find the residues linked to the ITD with a red dotted line, and click to select these residues. Note that selecting at this time is a responsibility instead of atoms.
Be careful when choosing. Deselect to click on the selected residue again. The selected residue (sele) was renamed to S1 using the method described above. Click S on the S1 line to select sticks, and C to select by elements.
Click L to select residues to display the residue name. In this example, it was found that one of the N contains 3 hydrogen bonds and two of them can find the amino acid residue attached to it. The other cannot be found because the hydrogen bond may be formed with water molecules, and the water molecules are in pdb. Only one O is used in the file. The stick display mode does not show the water molecules. Click on the all line S to select nonbonded. At this point, you will see a water and N form a hydrogen bond.
Click on the numerator blank, then click on the water molecule and change its name to w. Click H in the all line, select lines, then select nonbonded, and remove these display methods to leave only the cartoon. Click w line S to select nb-spheres.
5, the final finishing work
Reconstruction of residue name position: Click 3-button viewing in the lower right corner to convert to 3-button viewing editing, so you can edit and modify the pdb file. We can modify the position of the label to make the display clearer, then adjust the viewing angle. Until the display is satisfactory, you can save the picture at this time, the path is file>save image as>png.
In order to get higher quality and more beautiful pictures we can continue to process the menu bar according to the following path:
Setting >cartoon>highlight color;
Setting > cartoon >fancy helix;
Setting >transparency> cartoon > adjust the transparency to 50%;
Setting >label>size (adjust the label font size);
Display>background color>white (the background is set to white);
At this point the image in the window should not look good, we can try to click Draw/Ray in the upper right corner.
Choosing Draw will be faster and take up less computer resources. Select Ray and render it to a higher degree. Here I choose Ray.
Wait for a while, after you finish, you will find that the picture is clear and more solid. At this time, don't click on the picture again, save the picture quickly.
This will give you a picture showing the hydrogen bonding between the ligand and the protein-related residues.
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