I downloaded a protein from the PDB and realized it was bound to two native ligands. So, I wish to know why the protein was bound to the two native ligands and not one.
Enzymes or proteins have the ability to bind ligands to the binding site region, and a protein or enzyme may have multiple binding site regions
Some enzymes are multifunctional and catalyze more than one reaction. For example, MtmC in the mithramycin secondary metabolite pathway reduces one substrate and methylates another. Perhaps your protein is similar?
Dear Augustine, I think you should check whether the 2 ligands are same or different. Sometimes a ligand (if same) can bind to protein at two different protein binding sites. Also, most of the times, PDB files have 1 main ligand which inhibits the protein and other ligand act as cofactor (mostly ADP, ATP, GDP, GTP). Some ligands are added to the protein to stabilize the protein for crystallography. Mostly all the information is given the literature accompanied with the PDB.
Proteins have multiple binding sites depending on their function. For example, some enzymes require metal ions to act as ligands for their catalytic activity.
Thanks very much to everyone who bothered himself to answer my question. Your answers have really been of great help. Thanks very much
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