Re: [ccp4bb] ligand binds to one molecule

2022-03-06 Thread Dom Bellini - MRC LMB
I dont think it is necessary to prove what others have said so far, but if you would like some concrete evidence to support those statements: we cocrystallized a protein together with a small peptide, producing a crystal with for molecules in the AU but only one promoter showed clear density f

Re: [ccp4bb] ligand binds to one molecule

2022-03-06 Thread Oganesyan, Vaheh
Well, there is almost nothing left to suggest, but one. Try co-crystallizing. While in solution molecules will have more flexibility to adopt a conformation that fits ligand bound state better. When soaking there might be restrictions on conformational changes needed for better binding due to al

Re: [ccp4bb] ligand binds to one molecule

2022-03-06 Thread David J. Schuller
I think it would be a mistake to generalize. I have seen a situation in which 1 of 4 sites was occupied, the ligand was not included in the crystallization solution(which means it must have been bound beforehand) and the site participated in crystal contacts. I do not doubt that examples of the

Re: [ccp4bb] ligand binds to one molecule

2022-03-06 Thread Palm, Gottfried
Dear all,   I don't think, there is much to add to the statement of Bernhard or James that different protomers in the asymmetric unit (must) have some difference in there contacts and therefore often in their conformation. What it doesn't answer is a chicken or the egg question: do the differe