
Hello, My name is Benjamin Horsman and I am a student at the University of Toronto. I have what should be a basic (possibly naive) question regarding protein modelling that I was hoping you might be able to answer for me or point my in the right direction. I have been studying the structure of a bacterial protein complex, trying to understand how it interacts with several known binding partners. The complex is known to be a hexameric homomultimer. Recently the structure of the subunit protein was solved. However, only the monomeric form of the protein was determined, and the corresponding PDB file does not contain coordinates for the multimer (i.e., no BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a model of the hexameric complex for visual inspection and for some docking studies. What would be the best way to accomplish this? There are several structures in the PDB of hexameric protein complexes composed of subunits with very close structural alignment to my protein of interest, differing in two regions of the protein that are outside of the multimer binding regions. I believe that my protein complex posses very similar or nearly identical geometry to these known complexes. Is there any way to basically insert my protein into this geometry? Can this be done in Chimera? If not, is there any program or web server that allows this to be done? Or are you aware of a better way to get this done? Thank you for your time. Any help is greatly appreciated. Benjamin Horsman