[gmx-users] pdb file problem

[Justin A. Lemkul]

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,
> 
> 
> 
> 

-- 
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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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