i have a protein with two binding sites for a ligand. I have chemical shift information and crystallographic information about both binding sites.
I tried some ways to model two ligands binding the protein by defining three molecules (protein and twice the ligand), but it did not start the calculation it also did not give out an error, at the page where I entered the residues involved in binding of each site it did not let me proceed further and also it did not give me an error what I should correct.
so far i tried to model the ligand separately in the two binding sites but is there a way to set the ratio to 1:2 and get out a model with two ligands bound?
thanks a lot
Are you using the 2.4 server?
Is the ligand and binding sites are similar you can also simply only model one binding site.
If you do both you should try to have each ligand targeted to a specific site (the 2.4 server allows for that)
thanks für the fast reply
yeah i am using the 2.4 server. the binding sites are not similar. so i already modelled the ligand to each site separately and that worked really fine. I was just wondering if there is a way to define that there are two binding sites for a ligand and get out one pdb file with the protein having two ligands bound…
You can indeed do it.
In the 2.4 server you can tune the partners molecules when defining the active residues
ah I am glad thisis possible how exactly can i tune them?
what i tried is selecting three molecules and then using the ligand twice and selecting online protein ligand interactions…but as i descirbed before somehow it did not let me proceed further…without error notice…
Errors and warning will appear on the top of the window.
Also you will need expert or higher access level