I want to model a heterotrimer consisting of proteins A, B and C, where the structure of the A:B complex is already known, and C should be modelled. There is a known structure of another structure made of proteins D, E and F, where D and E are homologous to A:B (and can be easily spatially superposed) and F is homologous to C.
Do I have to work with restraints or is there a way to set a PIR file using the A:B and D:E:F complexes as "knowns" so that Modeller can assume that it must build an A:B:C complex so that A:B would be in the equivalent positions to D:E (but should of course be nearly identical to the A:B x-ray structure more than the D:E structure, since A:B is the real thing) and C must be modelled using F as template and be in the position it would occupy in the D:E:F structure?
To add insult to injury, although C and F are homologous, there is a better template, G, for it in terms of identity and alignment size. So the ideal solution to the problem would be:
A trimer consisting of A:B:C where A and B are knowns, C is modelled against G, and the A:B is positioned against D:E and the C model against G is positioned against F in the known D:E:F structure.
I hope my message is not too confusing...
P.S.: I already tried to separately model only the protein C against G and then using SSM to superpose the C model against F and the A:B complex against D:E, but that would produce some serious clashes, so I really need to build the whole thing on modeller.
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