Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.
So, it's not actually that carbonyl group is detached from the ligand? Otherwise I would suspect a radiation damage... Pavel. On 3/9/11 8:55 AM, Pompeu,Yuri Alexey Andreiw wrote:
Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.
Could it be bonding a water molecule which is not modeled, which in turn is binding the protein (water-mediated H-bond)? You don't mention the resolution of the structure or whether or not waters were modeled, or how unambiguous is the orientation of the ligand. And what did the average kick and SA composit omit-map prior to modeling in the ligand show that led you to be really lost? Perhaps the ligand is not there at all? If the density is really ambiguous it may not be possible to build the ligand with certainty, but looking at the H-bonds in different orientations as you are doing could be a basis for preferring one over another. eab Pompeu,Yuri Alexey Andreiw wrote:
Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.
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On Wed, 2011-03-09 at 11:55 -0500, Pompeu,Yuri Alexey Andreiw wrote:
it is not experiencing interaction in the form of H-bonds. Which I think is concerning.
Well it should not be. There are two possibilities: a) the carbonyl in question is facing solvent. Depending on resolution/degree of solvent disorder you may or may not see the water molecules that make hydrogen bonds b) the carbonyl in question is facing protein. In this case upon binding you simply lose a hydrogen bond that ligand was making to solvent. It is likely to cost some free energy, perhaps 1-2 kcal/mole, but other interactions may be more than enough to produce binding at whatever levels you observe. Of course, it is also possible that you are not modeling it right. Depending on resolution, quality of the map and internal symmetry of the ligand molecule, it may be possible to come up with alternative docking mode. You can get better (more specific) advice if you show your data to an experienced crystallographer. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
participants (4)
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Ed Pozharski -
Edward A. Berry -
Pavel Afonine -
Pompeu,Yuri Alexey Andreiw