Hello Rex,
Just a few biologically-related ideas that may support modeling the planar conformation.
I'm not sure if the protein you're working with has enzymatic activity, but is it possible that the ring strain is indeed real and may be a part of the reaction mechanism? Are any parts of the protein in contact with the flattened ring in such a way that they might be "pushing" or "pulling" the ring into the planar conformation?
Best,
Mike
----- Original Message -----
From: "Rex Palmer" <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, August 16, 2010 9:44:39 AM GMT -08:00 US/Canada Pacific
Subject: [ccp4bb] Lactose refinement
We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes .
Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm?
Rex Palmer
Birkbeck College
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Michael C. Thompson
Graduate Student
Biochemistry & Molecular Biology Division
Department of Chemistry & Biochemistry
University of California, Los Angeles
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