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[ccp4bb] Unidentified ligand (electron density) found at active site |
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CCP4bb navigationCCP4bb <-- 2007 <-- December 2007 <-- 05 December 2007Subject: Unidentified ligand (electron density) found at active site From: Ronaldo Alves Pinto Nagem nagem {- at -} ICB {- dot -} UFMG {- dot -} BR Date: 2007-12-05 I attached a sketch of my ligand. I realized it could be a di-peptide GlySer, but still, other potential ligands are possible and I have not a clue. The crystallization condition contains MIB buffer (sodium malonate, imidazole and boric acid) and PEG. As far as I know none inhibitor were present during purification. One important point about the ligand is that I believe the position occupied by the serine carboxylic group (in the di-peptide scheme) is indeed a charged group. Apart of that all positions and configurations might be possible (only using C, N, O and H – I did not see the presence of sulfur nor heavy atoms). Thanks again for all tips and suggestions and we will probably try mass-spectroscopy. Here is the summary (so far) for my previous question. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)? 1) from gbirrane@bidmc.harvard.edu Send a picture to the BB and someone might recognize it. 2) from artem@xtals.org If you send a picture of this stuff to the list, I bet someone may recognize it :) I think it's called 'distributed computing'. On a more serious note, a pharmacophore matching routine would do what you need, but you'd have to convert from E.D. to a 'blank pharmacophore with all property parameters set exactly to 1. Unfortunately, I don't know of any non-commercial programs for that stuff... --------------------------------------------------------- Prof. Dr. Ronaldo Alves Pinto Nagem Universidade Federal de Minas Gerais Instituto de Ciências Biológicas Departamento de Bioquímica e Imunologia Av. Antônio Carlos, 6627 - Caixa Postal 486 Bairro Pampulha - CEP: 31270-901 Belo Horizonte, MG - Brasil Tel: +55 31 3499-2626 Fax: +55 31 3499-2614 E-mail: nagem@icb.ufmg.br CCP4bb navigationCCP4bb <-- 2007 <-- December 2007 <-- 05 December 2007 |
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