We do not yet have the capability to link to anything other than ASN,
THR or SER on the website. We have parameters also for proline, but
the website doesn't support it. We only make available on the website
structures for which we have parameters that have been validated for
that purpose. We are considering allowing builds of other systems,
but we would not be able to provide files necessary to run a
simulation. It takes a bit of work to ensure that the parameters are
made properly.
Ignoring that entirely, I downloaded 1pt2 and took a look at that
residue in context. It is quite buried in that crystal structure.
Because of this, you should proceed very carefully when attaching
anything to it: the forces the structure would be under during
minimization could easily cause severe distortion of the protein or
the sugar. If that site is naturally glycosylated, then it seems
likely that either the protein distorted during the crystallization
process or the glycosylation occurs before the protein is completely
folded.
On Fri, Oct 2, 2015 at 12:28 AM, Surasak Chunsrivirot
<chunsrivirot.gmail.com> wrote:
> Hi,
>
> I want to build a structure of levansucrase (1PT2) with a fructosyl residue
> attached to Asp86 as in the attached picture. I tried the glycoprotein
> builder website but it doesn't allow me to choose Asp86 as my point of
> attachment. It only allows N-linking and O-linking glycosylation sites.
>
> I would really appreciate if anyone could help give me some
> advice/suggestions on how to build the structure of levansucrase (1PT2)
> with a fructosyl residue attached to Asp86. Thank you very much for your
> help.
>
> Regards,
> Surasak
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Oct 03 2015 - 21:30:04 PDT
