Hi all,
I would like to research on the effect of PG on some membrane protein using computational approaches. I need the pdb file of the following sequence:
NAG-NAM (L-Ala, D-Gln, L-Lys, D-Ala, D-Ala)
I have already searched from RCSB Protein data bank and pubchem database, but not been able to find it.
Could anyone help me please? And advise me what I should do?
Thank you in advance
There are structure of proteins in complex with NAG-NAM and one example can be found in the article displayed below:
Article The mechanism behind the selection of two different cleavage...
What you can do is to open the PDB file and delete the protein leaving the NAG-NAM, save the file and then try using this for your computational approach/es.
Or try the Cambridge Structural Database to find out whether there is a NAG-NAM in isolation !
Dear Bubacarr,
I would like to thank you so much for your answer.
I have read the paper and downloaded the pdb of NAG-NAM. However, this pdb file does not contain pentapeptide.
Could you please tell me if I can use NAG-NAM molecule as Peptidoglycan molecule for performing my simulations, or I need to attach a pentapeptide molecule to NAG-NAM using Molecular modeling software like Guess View?
In PDB you can find proteins in complexes with their ligands, not the structure of the peptidoglycan alone. If there isn't such a structure yet, nor in PubChem, you will have to create your own pdb file, starting with drawing the structure, conversion, energy minimization etc.
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