Where Is My Ligand? How Can I Construct A Ligand Bounded To A Homology Model?

Question

[laemtao]

I'd like to add a FAD|NADP ligand on my homology model, but my template PDB (1lqt) doesn't have one..or at least I think so as I cannot view it in pymol.

How can I visualize my template's ligand(s) and take that spatial data to add a putative ligand site on my homology model?

Thanks, laemtao

Answer 1

[João Rodrigues]

The easiest way is to find a homology that has that co-factor / ligand and model it using MODELLER for example (heteroatoms can be defined as dots in the alignment). The hard way, if you do not have a structural template, is to dock the ligand in the binding pocket. You can do this with Autodock, HADDOCK (good if you have information on the binding site or on specific contacts between protein and ligand), or any other protein docking software.

In your case, you do have FAD in your template (chain A, residue number 2457 for example). Just use MODELLER and include it following these instructions.