Crystal structure of proteins sometimes come with ions which function as stabilizers of the structure. So when we want to prepare the structure which we obtained from PDB, do we need to remove the ion? For example for PI3k crystal structure (PDB ID 3L08) it has sulphate ion.
Vary with cases. In case of a crystalline water present in your structure file; yes you have to remove it and in case if your ligand present in PDB structure might play an important support factor role in binding of your experimental ligand inside the cavity then no need to remove that. With case of 3L08 SO4 ion has no external functional annotations like ZIG. Usually SO4 ion presence in a structure has a random binding and signifies no specific binding site. Removal of such SO4 ions will lead you the rightly prepared PDB file for docking purpose.
Hi,
I would not be so strict at removing all water molecules... ligand binding might be water mediated. If possible check carefully all structures available for your specific target. If you are lucky enough to have structures of complexes, try to see if waters are involved in ligand binding, this will tell you which water molecules might be important. Remove all other waters, bu try to perform parallel docking runs, with or without the waters you identified as important.
For SO4 ions, the same logic applies: if you think it is important for ligand binding, try with and without. If not, remove it (but keep in mind that the position of the sulfate anion will be ideal for binding a negatively charge part of your inhibitor... it might helps when trying to thinks about ligand optimization!)
Thanks for your suggestions. ive tried to dock using the protein with n without the sulphate ions. seems without them the docking result are better than with their presence. thanks again.
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