Hi Andrew,
I can only make a guess: As the atom that actually should be O1 is called
O4A, and all the other atom names look fine apart from a B added to the
them, it looks as if this residue was derived from a disaccharide, where the
XYP part was linked to O4 of another residue. But I agree
Hi Markus,
I had a brief look at the structure fragment that you had included in your
mail, and I don't think that you really observe these two conformations.
Stereochemistry of the A conformation looks fine, but the sugar in the
alternate B conformation is not an NAG but an NDG (i.e. it has
Dear Hailiang,
as Herman Schreuder already wrote sugars are quite likely to contain errors. We
are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group
to help crystallographers locating problems in sugars. There will be an update
soon, which includes checks for
Dear Enrico,
you can find information on PDB entries with carbohydrates in the
GLYCOSCIENCES.de database:
http://www.glycosciences.de/database/index.php
To find entries with O-Glycans linked to Thr you can use the substructure
search at
Dear Katherine,
I would like to add a futher point to this discussion: If you do model residues
with poor or no electron density, then you should be sure of what you are doing
and not just make more or less unguided guesses. This seems obvious but
unfortunately it isn't, at least not to
On Thu, 22 Apr 2010 10:13:40 -0700, tirumal ch_tiru...@yahoo.com wrote:
If you have a poor density (which I guess, generally is the case for large
glycoprotein structures) you have to depend on trial and error strategy to
get the right NAG conformation. I don't know how other refinement
Just a quick thought that might be a workaround solution within the PDB format
restrictions: In NMR structures there are often multiple conformations stored
in different MODEL sections - this should in principle be possible for x-ray
structures as well, shouldn't it?
Of course this is a waste
Dear Chris,
this is not an answer to your question but may be helpful anyway.
I checked your glycan with pdb-care at
http://www.glycosciences.de/tools/pdbcare/ and found what I already assumed
from looking at the image you had sent: Some of your residues feature a wrong
anomer. BMA303B is an
Dear Goran et al.,
when building O-linked glycans one should keep in mind that in contrast to
N-glycans there is no single core structure in O-glycans, but a variety of
different structures exist. Therefore, the NAG-SER linkage might be correct (if
it is an O-GlcNAc modification, which is
