Re: [ccp4bb] REFMAC restraints for carbohydrates

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Research Position in Structural Biology at Pfizer, Groton CT, USA
From: "Pandit, Jayvardhan" jayvardhan {- dot -} pandit {- at -} PFIZER {- dot -} COM
Date: 2007-06-13

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Subject: Buildling CCP4+Phaser in FC6
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-13

Subject: Re: REFMAC restraints for carbohydrates
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-06-13

you can use
http://www.glycosciences.de/modeling/sweet2/doc/index.php
to get a pdb file of your sugar

and after fitting in density and refinement use
http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/
to check the stereochemistry

this should identify if there is a refmac dictionary problem

your sugar is a "Core Fucosylated And Bisected N-glycan (N-Link 2)"
[see the sweet doc pages]

you can make the IUPAC notation in plain ASCII

a-D-Manp-(1-6)+

a-L-Fucp-(1-6)+

b-D-GlcpNAc-(1-4)-Asn

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+

a-D-Manp-(1-3)+

and drop this into sweet and get an idealised torsion angle(d) pdb

an o/p is www.ebi.ac.uk/~henrick/sug.pdb

unfortunately the original pdb output is not exactly pdb
you have to move the residue name column and the
ASN is labelled as UNK

the torsion angles are from the database
http://www.glycosciences.de/modeling/glycomapsdb/

if you want to check your fitted conformation with what is expected
(a lot more freedom than a ramachandran but basically
the same type of plots)

--
Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Buildling CCP4+Phaser in FC6
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-13