Hello Everyone, I am attempting to fit NAD to a 2.1 A lactate dehydrogenase structure I've built and I'm running into several problems:
1. I loaded NAD from the COOT monomer library and was able to fit roughly 2/3 of it into the density using the real space refine zone function but the nicotinamide moiety flies apart as a result of the refinement. My work around for this was to load another ligand and roughly fit just the nicotinamide ring then cut and paste the coordinates from the second ligand into the file for the first. I then merged the ligand with the LDH structure using the merge molecules function in COOT. I fit NAD to four different chains this way. Attempting to refine the ligands after merging also results in the ring coming apart. 2. I was hoping that a round of refmac would then refine the entire ligand and thereby neatly fit the crudely placed nicotinamide ring. When I run refmac it fits the first NAD fairly rigidly such that while it does fit the nicotinamide ring it knocks the adenine moiety out of place. The other three NAD's look like they imploded. The atoms are too close together resulting in a structure which looks nothing like NAD and which contains multiple carbons with greater than four bonds. I was advised to create a new ligand dictionary and attempt refmac refinement with it. I have created files using refmac in review mode, loading the NAD coordinates into Sketcher and running libcheck, the PRODRG server and downloading from the HIC-UP server. Running refmac with any of these libraries produces the exact same result. Trying to use the real space refine zone on the one ligand which didn't come apart gives me the error message "No Restraints Found!". I am completely stumped as to what to try next. Any suggestions would be greatly appreciated. Thanks! Larry Grant
