Dear Klaus and colleagues,
For an (obviously highly exciting) journal club I compiled this table a while ago. It might be of help when trying to fit PEG fragments of various length: With HO-(CH2-CH2-O)n-CH2-CH2-OH as the general formula for PEGs, the distribution of fragments in the PDB is as follows: n PDB-Id # of structures 1 PEG 324 2 PGE 176 3 PG4 288 4 1PE 138 5 P6G 86 6 P33 27 7 PE8 7 8 2PE 29 9 XPE 3 10 n.a. 0 11 12P 12 12 n.a. 0 13 PE3 7 14-20 n.a. 0 Keep in mind that for a (monodisperse) PEG400 molecule n=9, for PEG1,000 n=20, PEG4,000 n=88, and PEG 20,000 n=450. I haven’t tried whether the monomer library that Coot uses contains all these fragments (it does know “PEG”). You could still copy the molecules from their respective PDB entries though and create the library description yourself (with Sketcher for example). Cheers, Uli --------------------------------------------------------------------------- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) [email protected] <mailto:[email protected]> http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ <http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/> Von: Klaus Sengstack [mailto:[email protected]] Gesendet: Donnerstag, 12. August 2010 10:17 Betreff: PEG in the pdb? Hi everybody, I just solved the structures of an enzyme an some variants. In the active site cavity of each variant I found one or two fragments of PEG1000 bound. I used PEG1000 in the crystallization condition. Among the enzyme variants the number of non-hydrogen atoms of these PEG fragments varies between 7 and 19 atoms. Now I want to deposit the structures in the pdb and my question is, if I have to define each fragment as a single ligand (what would be a lot of work) or can I define them as PEG1000 molecules? Thanks. K.S.
