Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] how to model glycosylated residues?
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 08 January 2008
Previous message:
Subject: Re: resolution & R-free
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-08 		Next message:
Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-08


Subject: Re: how to model glycosylated residues?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-08
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)
ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd