Dear experts,
I am trying to find the molecular structures files (PDB/MOL/MOL2) for less studied cynobacterial toxins (e.g. Microcystin-RR and -YR).
I can easily find MC-LR fie in Protain Data bank, but other are difficult / impossible to find. I tried to modify the MC-LR structure but it exists quite a lot of rotamers for that amino acid that differs. Thus download the MOL/PDB file would be the easiest solution for me.
Thanks,
Ondrej
Hey Ondrej: If i am right MC RR & YR are the Microcystin variants and MC LR is a wild type protein ? if that is the case then you most likely wont find a PDB file, you have to go for homology modelling.
Thanks for all your suggestions. But I cant still find those structures anywhere... :(
Ondrej
You can search at UNIPROT database (www.uniprot.org/uniprot/) but if you can't find the 3D structure, you ill need to ab initio model the structure, there is two aways to do, using the I-Tasser server or Rosetta Software.
write on google the ligand name with the key words MOL file (for example: alpha-terpineol MOL file) click on the first link (in general ChemicalBook website) you'll find the database file of the compound. Click on its mol file and it will be downloaded.
For the proteins (receptors, enzymes...etc) search them on RCSB PDB website
http://www.rcsb.org/pdb/home/home.do
Thank you for your suggestion.
I have tried that, but I could not find the structures..
Ondrej
If there are several ligands, is there any ways to download all of them at once?
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