CCP4 bulletin board <[log in to unmask]> wrote on 04/22/2009 08:12:37
AM:
> Hi,
>
> Could someone point me to the best ways of building a non standard
ligand?
> I had PEG-400 in the cryo, and the density is about twice as long asthe
"PEG"
> that is in the monomer library.
>
> I can get the cif file for PEG-400 from prodrg (1PE). Just wondering what
is
> the best way to use it for importing molecule, real space fitting etc.
> Attached a photo of the density.
>
> Regards, Partha
>
>
Hi Partha -
PEG-400 is a mix of different lengths of polyethylene glycol, but the two
dominant species are probably the ones closest in molecular weight to 400
daltons. Those would be octaethylene glycol, with a molecular weight of
370, and nonaethylene glycol, with a molecular weight of 414. Your 1PE
molecule is pentaethylene glycol, which has a molecular weight of 238 - I
don't know why it's called "PEG400".
I built a molecule of heptaethylene glycol (MW 326) into a structure of
mine that had PEG 400 in the mother liquor (PDB code 1OXN - the ligand is
called P33). As I recall, I made an idealized molecule using InsightII,
then built it manually into the density using torsion_general in O, plus a
great many fiddly adjustments in the molecule's position and orientation.
For refinement, I let Refmac auto-generate a suitable dictionary file.
You could use my P33 molecule as a starting point for your density. I was
only convinced that my tube of density was PEG when I saw the regular
pattern of hydrogen bonds alternating with hydrophobic patches that the
modeled PEG presented to the protein.
Hope that helps,
Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
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