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:

  1. 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?

  2. 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?

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    $\begingroup$ Welcome to the site. 1) Did you check out the description of the structures? Of which organism are you interested in the wild type of the protein? 2) Yes you could. Why do you want to extract the ligand from a structure and dock it back? (This seems homework and could be only to you to practise how to use the software) $\endgroup$
    – llrs
    Apr 4 '19 at 10:05
  • $\begingroup$ 1) Yes, I did read the literature and it mentioned that 1GOF is belong to wild type but interestingly, I found another 2 structures (1GOG, 1GOH) that have the identical sequence as wild type (1GOF). That's why I confused which structure to use, btw the differences between these 3 structures are only their ligands. My question is since their sequences are identical, does it means that I could just use either one of them to perform docking? $\endgroup$ Apr 5 '19 at 1:45
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    $\begingroup$ All three structures are from the same specie but other species could have a different wild type. There is no rule why a single molecule can't be linked to several others but the structure might be different (or change when docked with other ligands). Yes you could use any structure to perform docking but the suggested structures could be different according to the initial state of the structure $\endgroup$
    – llrs
    Apr 5 '19 at 7:08

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