I have two very similar protein structures open in DeepView. One is a crystal structure containing a bound ligand, and the other is highly similar protein, which is capable of binding the same ligand.
I want to copy the ligand from one protein into the other, and see the effect on its structure.
The problem is, when I try and import the ligand from PubChem DeepView crashes.
Any help on how to incorporate the ligand into a new PDB (or RasMol) file would be appreciated.
Hey Joseph,
Try using Pymol. Once you have pymol, open your protein files and use the following command to align both those proteins.
align protein1, protein2
After that check if both the protein aligns very well. Once you have that. press the S symol on bottom right which will show you sequence. Select the sequence with your mouse and also select the ligand.
then go to Files-save molecule and check the sele "to select your molecule of interest" and save it.
To help you in a better way, please follow the video linked below:
https://www.youtube.com/watch?v=T0v1Dx6Yb-I
Joseph: PDBViewer is basically a visualization software. I assume that you have a PDB file with a protein and the ligand of interest and you are interested in knowing how the ligand looks like in a different, but similar protein. If this is the case: 1. Load one of the files. 2. Before loading the second file, make sure that you have clicked the option "magic fit onto first protein loaded" (Preferences > Loading molecule preferences). You will get both proteins aligned. You may improve the alignment (Fit > Improve Fit) 3. In the control panel (window>control panel) click off the column "show" for the protein with the ligand and go to the end of the column to click on only those residues (i.e. ligand molecules) of interest.
Now you have the ligand placed onto your protein. However (at least in the version that I have, which is not updated), it is just an image and you can not make any calculation or save the coordinates of the alignment. It is better to follow a similar procedure using UCFS Chimera (https://www.cgl.ucsf.edu/chimera/) because you can save the position of the molecules after alignment. Good luck.
Hello Javier,
Thanks for the good advice, I had already aligned / superimposed the two proteins with magic-fit and found them to be almost perfectly aligned (are therefore likely both binding the ligand the same way). But yes I would like to copy the ligand into the new protein structure - so I will definitely check out the Chimera software :)