I need a pdb file of the following ligand : tetrasaccharide-pentapeptide NAM-NAG-NAM(-L-Ala-D-iGln-L-Lys-D-Ala-D-Ala)-NAG . It is part of the peptidoglycan polymer
I think this link may come handy.
The Protein Data Bank
http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=FD70AFD2
searching from RCSB Protein data bank is good. you may obtain it very easily.
Hi Dr Yasser (HRY hope u r fine)
Please have a look on this article
http://www.jbc.org/content/289/34/23403.full.pdf
the authors in this article have docked the structure of TSPP generated by the program of PRODRG server due to the unavilability of TSPP
This is the link to PRODRG server
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/submit.html
you can try to draw the chemical structure and generate the TSPP using this server
Thanks dr Ahmed , I hoped I can find ready structure. Now I have to work on the polymer until the pdb , including drawing, conversion, check the chemistry and energy minimization steps.
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