CCP4 bulletin board <[email protected]> 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 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
