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Re: [ccp4bb] how to model glycosylated residues?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 08 January 2008
Previous message:
Subject: Re: How to refine large moleculars?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-08 		Next message:
Subject: Re: How to refine large moleculars?
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2008-01-08


Subject: Re: how to model glycosylated residues?
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2008-01-08
Hi Jiamu,
You can use Sketcher to make the library for Coot.
You'd better to get the PDB file from

http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/ .
Good luck!
liu

Jiamu Du wrote:
> Thanks for all the replies above. I have pasted the figure of the
> electrondensity map in the attachment. It seems I can fit two NAC
> molecules into the density. Any more suggestions are appreciated.
> The remaining questions is below:
> How to refine the NAC molecules in COOT or in O? It seems there is no
> LEGO and TORSION tools for sugar in O. Should I fit them into the
> density by rotate and translate each NAC molecule manually?
>
>
>
> On Jan 8, 2008 5:37 PM, Laurent Maveyraud
> > wrote:
>
> Hi Jiamu,
>
> just add the desired sugar residue (likely a GlcNAc for a
> N-glycosylated
> Asn) (ND atom of ASN linked to C1 of sugar. Refmac should handle it
> properly. If not you have to add aLINK statement in the PDB
> header. Take any
> glycosylated structure in the PDB as an example (eg ricin, 2AAI).
> Feel free to ask further if needed !
>
> best regards
>
> laurent
>
>
> -------------------------------------------------------------------
> Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
> Université Paul Sabatier Toulouse III
> I.P.B.S. UMR 5089 Groupe de Biophysique Structurale
> Département Mécanismes Moléculaires des Infections Mycobactériennes
> 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE
> Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
> -------------------------------------------------------------------
> ________________________________
>
> De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] De la part de Jiamu
> Du
> Envoyé : mardi 8 janvier 2008 10:00
> À : CCP4BB@JISCMAIL.AC.UK
> Objet : [ccp4bb] how to model glycosylated residues?
>
>
> Dear All:
> As mentioned before, I am working on a 2.6 A resolution structure.
> There
> might be a glycosylated Asn.
> I want to model some carbohydrate molecule into my structure.
> My question is how to model them? Should I treat them as small
> molecules?
>
> Best Regards.
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)
>
>
>
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)



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