Hi, Bond length and angle targets are defined based on the local chemistry and apply equally to small and large molecules. The Ramachandran distributions were defined via an examination of, basically, tripeptides. Your peptide model must be consistent with these prior observations to be considered reliable. If it is not there is likely something seriously wrong with your interpretation.
In addition, your model peptide must make chemically reasonable interactions with its partner. You didn't describe this aspect of your model, but this is equally critical in the evaluation of the model of a bound ligand. In my opinion the most likely explanation is that multiple conformations of the peptide are binding. Without seeing the density or being able to examine the data it is hard to generate possibilities. Dale Tronrud On 10/1/2017 2:20 AM, Meytal Galilee wrote: > Hi All, > I have solved a structure of a protein bound to a short peptide (11 > residues) at 1.9A. > The peptide fits the map perfectly, however, all of its residues are > either Ramachandran / bond length / angle outliers. > Fixing any of these issues forces the peptide to misfit the map > dramatically. > Is anyone familiar with short peptides outliers? Are these issues common > / acceptable? > Does anyone have an idea or suggestion? > Many Thanks, > Meytal Galilee >
