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[ccp4bb]: error in Refmac library?
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Dear collegues,
I am currently refining a glycoprotein with an N-acetylglucosamine unit (NAG)
attached to an ASN residue and L-fucose (FUC) bound to that NAG via an 1-6-
glycosidic bond.
Refmac5 automatically assigns a "BETA1-6" bond between FUC and NAG and writes
the following record to the coordinate file:
LINK NAG E 401 FUC E 402 BETA1-6
According to textbook definitions however I suppose that the correct assignment
should be "ALPHA1-6" (in agreement with the corresponding topology file of CNS
which contains a patch "A16L" for the alpha-1-6 link of L-fucose but no patch for a
beta-1-6 link and in agreement with synonym definition FUC = FUC-a-L in the refmac
library).
I this an error in the refmac library?
With kind regards
Karsten Niefind
----------------------
Dr. Karsten Niefind
Institute of Biochemistry
University of Cologne
Zuelpicher Strasse 47
D-50674 Cologne
tel.: +49/221/470-6444 (Secretary: +49/221/470-6440)
fax: +49/221/470-5092
E-mail: Karsten.Niefind@uni-koeln.de
Internet: http://www.uni-koeln.de/math-nat-
fak/biochemie/ds/ma/kni/inhalt_englisch.htm