Hi,I did a little bit of "modeling" in your density (starting from a nicotinamide ring, the positioned nicotinamide is enclosed). The middle part looks suspiciously like a 6 membered ring. Could it be a molecule in a half-chair conformation? There is only the blob that is perpendicular to the ring that would remain unexplained...
If it is indeed a molecule in a half-chair conformation then you'd need to ask a chemist what it could be.
Note that I did not try to distort the nicotinamide ring to a half-chair conformation
Blobology is a difficult branch of our trade... I've had a case where I had to state in the publication that a sodium (I think it was) ion had been introduced in the model to explain a density feature but that it wasn't known what this spherical blob of density in fact corresponded to.
Fred. Priscila Oliveira de Giuseppe wrote:
Hi, everyone, I solved a structure at 1.7 A. After fitting all residues into the model, I found an extra density at the catalytic site. The components of the crystallization condition did not explain it (crystallization condition: 40% PEG200, 0.1 M Tris-HCl, protein buffer: PBS) Neither substrates nor products of this enzyme fitted this density. I modelled two PEG molecules with half occupancy. They fitted very well, but I am not convinced that this is the best explanation. Does anyone figure out what this density can be? Attached to this e-mail I send the maps and a pdb file with the residues surrounding the ligand density. Thanks Priscila
nicotinamide.pdb
Description: Protein Databank data
