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: mbfro...@post.tau.ac.il <mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jan 7, 2013, at 11:48 , Felix Frolow <mbfro...@post.tau.ac.il
<mailto:mbfro...@post.tau.ac.il>> 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: mbfro...@post.tau.ac.il <mailto:mbfro...@post.tau.ac.il>
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jan 7, 2013, at 11:28 , Xiaopeng Hu <huxp...@mail.sysu.edu.cn
<mailto:huxp...@mail.sysu.edu.cn>> 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
