Hi Mariah, We have had one case of this, with two partially overlapping conformations of a ligand, which is not yet published.
Model in both ligand conformations. Then edit the PDB to give them the same Chain ID, but with alternative conformations for each atom, or each one that is different. You might try giving 0.5 occupancy to each for REFMAC refinement. In Phenix you can also refine the occupancy. Here is an example for the CAA atom of our drug. ATOM 7090 CAAADRG E 1 9.312 2.643 8.223 0.50 42.57 C ATOM 7091 CAABDRG E 1 12.707 2.133 -0.186 0.50 36.22 C Regards, Kendall -- Kendall W. Nettles, PhD Asssociate Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 On 1/12/09 6:52 PM, "protein.chemist protein.chemist" <pp73...@gmail.com> wrote: > > Hi, > > I had a question about flexibility in ligand binding in an enzyme active site. > Is it possible for a substrate/product analogue to bind in more than one > conformation in the active site. Since the ligand/enzyme interactions are > very specific I am a little confused about this. > Also which program would you use if you have to refine with alternate ligand > conformation. > Please mention if you have ever come across any paper that explains such a > phenomena. > Thanks a lot. > > Mariah
