Obtaining the target molecule is crucial. It only depends on the problem you are planning to solve. There are a couple of different possibilities that you can get your protein structure. The easiest one is RCSB Protein Data Bank. If you are looking for a protein molecule which is already scanned and published here, you are free to grab it and use on your experiments.
As you can see on the search box, it is possible to search via molecule name, PDB ID or even with author name. I will use a molecule which I used previously for a research. I will give more details about cleaning and preparing the molecule. But keep in mind that RCSB is not the only source for your target molecules. You can obtain your molecule from somebody who does X-Ray Diffraction or Nuclear Magnetic Resonance (NMR) for your preferred molecules.
In this case, I am choosing the PDB record of one of the MAO B molecule. Its ID is 2V5Z. After searching with this four character you can visit its page and download PDB file.
After downloading I have the file with name 2v5z.pdb file. Even though it includes everything we need it is not ready to use. First, let’s visualize it with PyMOL. You can download it for any platform.
Published PDB files may include some kind of missing information. But it is possible to add and remove incorrect parts even though we can just do computational operations. For example wavelength of the X-Ray is not suitable to detect all Hydrogen (H) molecules but it is quite easy to calculate correct positions of Hydrogens. Also when you open the molecule with a visualizer, you will see a huge molecule with two subunits and some solvent structure which is the artifacts of the creation process. Let’s check cleanup steps one by one.
- Open your molecule file with PyMOL. You will see the molecule file and the command prompt will be available for commands we have to issue.
- Rename the saved file and get rid of redundant information fields of PDB file:
save molecule.pdb, all
After saving the molecule you can find the file on your root directory of the user. Which could be different on different operating systems. You can use the search functionality of your operating system. molecule.pdb will be the filename if you have not got any error message. Please pay attention to the comma just after the filename.
3. Remove hydrogens by typing exactly this command: (our example may not need this but you will need it for almost all times.)
4. Remove solvent by typing exactly this command:
After removing solvent the molecule view will be more clear and small red dots disappear.
4. Select the redundant subunit by typing exactly this command:
5. Rename the selection as it is shown in the screenshot. Click A on the “sele” item of the side panel after that you will see “rename selection” on the list. Click it and pay attention to the top left of the molecule view. Just rename it as molecule_subA. Now it is easily selectable. You can do the same for subunit B.
6. Remove oene of the subunit. I will remove B. So I issue this command:
save molecule_subA.pdb, all
(This could also be done via the side panel)
7. Remove ligand from the molecule.
We are very lucky to have a Safinamide molecule is buried into our file. We will not eliminate it and have the target molecule cleaned up because of the initial structure of the molecule our cavity in the most suitable shape for the docking. We could have saved the file into another pub file but that will be another step of this series so we will just remove it now.
If you open the PDB file with a text editor, you can notice SAG and FAD residues. The FAD is part of the MAO molecules. But SAG is not. It is naturally docked now. Be would like to remove it. Just deleting the SAG lines from the file is enough but I will show the PyMOL way:
8. Save the file. I will rename it as target.pdb since we will use it as out docking target.
save target.pdb, all
In the next section of this series, I will describe who to get the safinamide out of this molecule and other ways to create a ligand from scratch.
NEXT: Obtain or Create the Ligand Structure