In such a case select one chain at once rather than the entire structure of insulin receptor. If the co-crystallized ligand is present in all chains lets say A and B, in that case, docking can be performed on any one chain. If not, then check the chains contributing to interactions with co-crystallized ligand. If no co-crystallized ligand is available, perform binding site prediction and then continue with docking on one particular binding cavity of one chain.

Don't use the whole receptor

Instead use the protein chain where the active site remains.

Regards

Thank you so much for all the answers. I'll try dock with part of the insulin chain. Hope everything goes well. Jobin Thomas Nachiket Joshi Shiwa Chaubey