Hi All,
My question is concerning geometry of NAGs in a glycoprotein structure.
I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs
linked to Asn at 3 different places. NAGs and Asn-NAG links are refined in
Phenix.refine as per the Phenix dictionary.
However, when submitting the structure to the PDB, internal validation of PDB
found that NAGs at 2 places have geometry problems (atoms surrounding the C1 of
NAG are in the same plane). What I learned from Phenix bulletin board is that
the refinement program is probably fixing the NAG into a local minimal
structure to fit to the density the best (I have OK density for sugars) and
that's causing the problem.
So, I tried to fix the geometry of NAG while refining, so that the refinement
does not change the geometry of the sugar. But, still the internal validation
of PDB found the same problem with the sugars.
Then, I tried replacing the NAGs with ideal monomers from Coot. Still, the
problem persisted. PDB annotator's suggestion is to get the NAG coordinates
from HIC-Up and try refinement in another program.
I am wondering if any one else noticed (or had ) a similar problem with NAG
geometry using either Phenix.refine or Coot. What baffles me is that the
ideal NAG from coot dictionary did not pass the internal validation of the PDB.
I would appreciate if any one has any suggestion (other than trying a different
refinement program) to get around this problem. Is there a way to compare the
NAGs in your structure to the ideal and get to know what to fix ?
Thanks in advance
Tirumal
