Currently, I am working on Galactose oxidase enzyme for protein docking and I am totally new to it. I have to study how mutation on specific residue will make mutated galactose oxidase better than the wild type. My questions:
There are so many structure available on PDB, how to know which structure is the so called wild type structure? Is the structure with PDB Code: 1GOG belongs to wild type?
I was requested to extract the ligand(substrate) out of the structure and docked it back. But seem all the structures available on PDB do not complexed with ligand. For what I know, the substrate for galactose oxidase could be D-galactose. Could I use the galactose oxidase structure from pubmed and dock it to the enzyme? Btw, what is purpose of extract the ligand out and dock it back?