New to crystallography...I want to compare ligand binding in a crystal structure to one generated using NMR. I have tried the pdbsum and the pisa servers but the hydrogen bonds that are identified differ from the ones identified in the publication of the NMR structure, perhaps because they used the NMR program MOLMOL for analysis? Although I can use pdbsum or pisa to identify the ligand bonding mechanism in the crystal structure...I'm not sure whether it would be correct to compare this with those identified in the publication of NMR structure since I know that using these servers the bonds identified in the NMR structure also differ..so I can't be sure if any difference identified would be a true difference or just a difference in analysis method. Or perhaps these servers aren't suitable for analysis of NMR structures? Any advice much appreciated!
You can manually identify hydrogen bonds in NMR structures as they usually come with hydrogens in PDB file. If H - O distances are less than 2.0 while N - O distances are less than 3.0, they may be right. Also, NMR structures differ from X-ray structures because 1) NMR is usually used to determine proteins in solution while X-ray structures are from crystallized sample, 2) NMR structure determination is just different from X-ray. It is not like what you get what you see. It is pure computational energy minimization by slow simulated annealing steps using distance information obtained from NOESY spectra. So, they can be different.
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