Your best option is to download the structure files from the PDB and use a standalone program like VMD, PyMOL, or JMol. All of them are well suited for this task. There's a classic command-line program called ProFit as well. There may be web services available but you'll ultimately want a visualization tool.

If you are trying to superimpose a protein strucutre on a co-crystallized structure with a ligand and see interactions mediated by new ligand, you may use the tools mentioned by Kraut. I would also like to point you towards the Structural alignment software page at Wikipedia. I would like to recommend a particular tool MinRMS which Computational expensive, but more accurate structure alignments and SuperPose protein superposition server.

You may also explore the possibility of docking here. For example, if want to see how a ligand can fit in to a protein without known co-crystallized ligands, you may also perform a docking using your structure and the ligand using docking programs (for example AutoDock, ZDOCK) will generate the structure. If you need to understand the structural interaction in detail, you may use the binding site information from your co-crystallized structure and perform a flexible docking.

You can download co-crystallized structure structures deposited in PDB, you can download them from PDB in default assembly and quaternary assembly from PDB. For example here is the link to access 3EAX at PDB and PDBe. Ligands are defined using the HETATM records.*

Try out symmdock. here is the link. http://bioinfo3d.cs.tau.ac.il/SymmDock/ Hope this will help you

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http://www.molsoft.com/icm_browser.html