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But I think the original poster meant partially overlapped after applying the ncs- operator- i.e. they are not ncs related but occupy partly the same position (in the two non-overlapping copies of the binding site). Then I guess it depends how clear the density is- If the density is not very clear and if the protein residues of the active site do follow ncs, I would try rebuilding ligand b to match a and (separately) a to match b and refining with ncs applied to the ligand; and see if the resulting fit looks just as good. eab Joel Sussman wrote: > Dear All, > Something like what Felix wrote is seen in the crystal structure of *recombinant human acetylcholinesterase* (*rhAChE*) > (PDB-ID: *3lii*), with two molecules are seen in the asymmetric unit. > * In one molecule, the active-site gorge (where inhibitors normally lie) is occupied with part of a peptide loop from a > symmetrically related rhAChE. > * While the corresponding region of the other copy of rhAChE is void of this peptide. > See figs 15-16 in: > Dvir, H., Silman, I., Harel, M., Rosenberry, T. L. & Sussman, J. L. (2010). "Acetylcholinesterase: From 3D structure to > function" /Chemico-Biological Interactions/ *187*, 10-22. > * So, in essence, no reason to ever assume that two copies in asymmetric unit will be identical, or have identical > inhibitors bound, or 'surrogate inhibitors' (like in this case) bound. Sometimes differences are due to difference in > crystal packing > Best regards, > Joel > > > On 7 Jan 2013, at 11:58, Felix Frolow wrote: > >> I apologise for typing blinbly: >> " if one is in, the second can't be" >> FF >> Dr Felix Frolow >> Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology >> Tel Aviv University 69978, Israel >> >> Acta Crystallographica F, co-editor >> >> e-mail: [log in to unmask] <mailto:[log in to unmask]> >> Tel: ++972-3640-8723 >> Fax: ++972-3640-9407 >> Cellular: 0547 459 608 >> >> On Jan 7, 2013, at 11:48 , Felix Frolow <[log in to unmask] <mailto:[log in to unmask]>> wrote: >> >>> Why not? They can be mutually excluding! If one is in, the second can be. This phenomenon brakes a local symmetry. >>> FF >>> >>> Dr Felix Frolow >>> Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology >>> Tel Aviv University 69978, Israel >>> >>> Acta Crystallographica F, co-editor >>> >>> e-mail: [log in to unmask] <mailto:[log in to unmask]> >>> Tel: ++972-3640-8723 >>> Fax: ++972-3640-9407 >>> Cellular: 0547 459 608 >>> >>> On Jan 7, 2013, at 11:28 , Xiaopeng Hu <[log in to unmask] <mailto:[log in to unmask]>> wrote: >>> >>>> Dear All, >>>> >>>> We recently resolved an enzyme/inhibitor complex structure. The enzyme contains two NCS related active site and we >>>> did find extra density in both of them.However we observed that the two inhbitor moleculors are not NCS related, but >>>> partly overlaped if make a NCS moleculor. Has anyone else observed this before? Thanks for any help and suggestion! >>>> >>>> >>>> Best, >>>> >>>> Xiaopeng Hu >>>> >>> >> >