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Finding the Active Site Pockets of a given Protein Molecule




Working of PyMol and Loading the .pdb file


Installation instructions and the links to download the software or the data can be obtained through the simulator tab


When the molecule is loaded into PyMol the molecule can be controlled by mouse, with three buttons, left, middle (pushable ball), and right. The left button is used to rotate the molecule. Middle button is used to move the molecule and the right mouse button is used to move the molecule in z axis that is to zoom in and out.


Load the downloaded PDB file into PyMol (Figure 1).



Figure 1: Screenshot of standard file chooser of PyMol to load the PDB file


File → open→ choose the PDB file where it is actually located. User can also load the file through command line using the command load <file path>       E.g., “load C: Downloads1UBQ.pdb”


By default, the loaded PDB file structure will be shown with line representation in PyMol (Figure 2).


Figure 2: Screenshot of PyMol with a loaded molecule


We can see two rows on the right side of Figure 8, labeled as ‘all’ and ‘4AX9’ where we can change individual appearance of a molecule as well as all molecules together. If there are multiple molecules, user can also select every molecule or object at same time.


User can also see A,S,H,L and C labels in the two rows as different columns, these alphabets implies, Action , Show , Hide , Label and Color respectively. We can use these GUI elements or the user can give commands to get performed actions (Figure 3).



Figure 3: Screenshot of the Internal GUI buttons


A protein named ‘thrombin’ which forms a complex with “Napsagatran” ligand molecule, has been downloaded from the protein data bank. Through the detailed annotation of the cited paper or journal article in protein data bank, it has been reported that thrombin has different amino acid residues which act as active sites like Serine (ser 195th residue), Glycine( Gly 219th and 216th residue), Aspartate(Asp 189th residue), Tryptophan ( Trp 215th residue) and Tyrosine (Tyr 60th residue). These residues bind to the ligand molecule “Napsagatran” (N5N).


To view these active sites, hide all the objects loaded into PyMol by using the command “hide”.


Represent entire protein with surface representation, setting with a 50% transparency. Select the object protein molecule, show  surface turns the entire protein molecule into surface representation. Alternatively use the command “show surface, 4AX9”.


Figure 4: Surface representation of a protein molecule


User can set up the Transparency by choosing settings in the standard menu bar , thus choose submenu transparency , surface with 50% , alternatively by the command “set transparency 0.5” (Figure 5).


Figure 5: Representation of transparent protein molecule


The protein databank will provide the information about the ligand molecule bound to the protein. User can know the ligand molecule name. Here the ligand molecule name is “N5N” (Figure 6).

Figure 6: Information about ligands


Use the command “select” to view the ligand molecule. The syntax to view the “N5N”ligand is “Select ligand, resn N5N” (selecting the ligand molecule N5N with the object name as ligand). Thus we can observe small pink dots on the molecular viewer, using internal GUI selecting ligand object, and show it as “sticks” such that ligand can be viewed. Then disable the ligand by clicking on the ligand object, pink dots disappears (Figure 7).


Figure 7: Ligand molecule bound to thrombin protein


Finally, the active sites can also be selected using the select command.


“Select activesite, (resi 189,195,215,216)”, thus change the representation and color of the activesite object to differentiate the ligand object and active sites of a protein molecule (Figure 8).


 Figure 8: Active site of the protein molecule, where the ligand is bound


We can also label the residues of active sites by ‘L’ button in internal GUI, and can show the residues (Figure 9).



Figure 9: Labeling of active site residues.



This experiment uses :The PyMOL Molecular Graphics System, Version Schrödinger, LLC.





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