I've often wondered about PEG (and, I guess, other synthetic polymers): wouldn't it just be better to define the monomer, and then model a chain of however many monomers you need?
T Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 25 Jan 2017, at 17:21, Edward A. Berry <ber...@upstate.edu> wrote: > > Uma's use of quotes around "di" suggests a related question about PDB > convention. It was my (perhaps not very good) understanding that ligands > should be identified by what is actually present in the crystal, and not by > what can be modeled. For example endogenous ubiquinone is likely to be UQ50 > (depending on the species) but most of that 50-carbon side chain is hanging > out in the lipid or detergent and completely disordered. Still we should use > the ligand identifier for UQ50, even though codes exist for UQ with 5 or > 10-carbon side chains that are much better accommodated by the density. > > If that is the case, one should not use the pdb identifier for diethylene > glycol (PEG) when PEG4k was the precipitant, unless you believe that the > binding site has specifically selected diethylene glycol from an extremely > broad range of polymer lengths in the added material. Using the identifier > for a much longer PEG will result in a large number of "missing atoms" listed > in the report, but would eliminate the unreasonable assumption that PEG > fragment models must always end with a terminal oxygen. > > Even if that is the rule, I would agree that PEGs would be a good place to > ignore the rule. Since PEGs have a MW distribution, it is impossible to know > exactly what is bound and it may be different in different unit cells. If you > are not going to get it right no matter what you put, you might as well put > something that fits. > eab > >> On 01/25/2017 09:51 AM, Uma Gabale wrote: >> Dear all, >> Thank you very much for your replies. It is a PEG, a "di"ethylene glycol to >> be precise, in most chains. >> Best regards, >> Uma. >> -- >> Uma Gabale, PhD >> Research Associate >> Molecular and Cellular Biochemistry >> Indiana University Bloomington >>
