Does anybody know the pdb codes with proteins with O-linked
sugars on THR.
I support a program to help interpret sugars in poor electron density
by stabilizing links. Coot helps a bit but branching poses a problem.
Rather than based on distance like coot operates at present it should be
best
if one could specify the type of link.
I have crystals where sugars are in poor electron density. I can recognize
sialic acid moieties at a crystal contact with symmetry related molecule,
but fitting the weak density for the sugars leading to the crystal contact
is
almost impossible.
There are good reasons to combine knowledge of normal human glycosylation
with
weak electron density to produce a reasonable model. With natural products
and
heterogeneous sugars, the density in never going to be fantastic except
for the few
sugar moieties close to the protein. Yet interpreting all existing density
may be a step
better than outright modeling.
Enrico.
On Thu, 10 Mar 2011 09:45:57 +0100, <herman.schreu...@sanofi-aventis.com>
wrote:
Dear Hailiang,
While apparently no response came, here my 2 cents:
Even if there would be an automatic utitility to generate links based on
distances, I would never use it. Either the sugars have been properly
refined and then the link cards are present in the pdb file, or the
sugars have been fitted manually and may have been real space refined in
coot or some other model-building program. In this case, the sugar
positions are likely off, since sugars are very often rather disordered
and have poor electron density. In this case distance-based link
generators very likely will make wrong connections. I just cut and paste
link cards from an other pdb file and manually edit them. I eagerly
await the moment there will be a create link option in coot, where you
just click on the two atoms to be linked and the link card gets
generated.
Best,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Hailiang Zhang
Sent: Wednesday, March 09, 2011 1:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Automatic LINK generation
Hi there,
I am trying to build the LINK information in PDB header for
sugar-containing protein, and I am wondering whether there is some
utility in CCP4 (or any others) can do it automatically (eg by measuring
inter-sugar distances). Thanks in advance!
Best Regards, Hailiang
--
Enrico A. Stura D.Phil. (Oxon) , Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab
LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE
http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura
http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html
e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
