How do you predict protein's binding sites?

We do not have to predict binding sites in the proteins which are well-studied and whose structural details are available. You can find them with the associated literature in the PDB entry of protein itself. When you open a specific PDB entry, you can find a section named ‘Literature’ on the same page, which consists of the research paper(s) about the structure of that protein (PDB entry). This paper illustrates all the details about the catalytic residues or binding sites within that specific protein.

You do not have to use any online server because it is a tedious task, it will give you multiple binding sites but you would never know which one you want to bind your molecule in. Therefore, just go to PDB and when you will open 3BJC entry page, you will find the associated literature about it. You go for predicting binding sites only when there is no study available related to the structural details of a protein.