benrezkallah djamila wrote:
Hello Everybody;
I have a problem with The 2PU3 pdb entry (download from www.rcsb.org
<http://www.rcsb.org>) ; the download file gives for certain residues
such as residu 25 : SER (and others in the pdb file), two different
positions for the atoms of the residu.
ATOM 18 N ASER A 25
ATOM 19 N BSER A 25
ATOM 20 CA ASER A 25
ATOM 21 CA BSER A 25
.
.
.
why atoms are twice given, with two different positions?, are there two
possible conformations for the residue?
This is usually the case when the crystal structure is poorly resolved in this
area. Refer to the paper that corresponds to the structure for details on what
was happening.
Please, it will help me much to know what atom to choose for the
corresponding residue
( for exemple CA A SER 25, or CA B SER 25), because I need the right
coordinates for a further study.
I would separate out the two possible configurations and run simulations of
each. More than likely, at physiological temperature, you'll observe both
configurations, indicating that either starting orientation is probably valid.
If you do the simulations to prove it, then you can handle reviewer concerns
with no issue.
-Justin
Sincerely yours,
Djamila Benrezkallah,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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