Great reminder. But there are real non proline cis peptide bonds, including highly conserved motifs in active sites, e.g. 3UAO and its homologs. I would hope these don't get "corrected".
Roger Rowlett On Feb 16, 2015 5:09 AM, "Tristan Croll" <[email protected]> wrote: > Dear all, > > > My apologies for the spam-like nature of my post, but I would like to > draw your attention to an important issue (outlined in an upcoming short > communication to *Acta D*, which will appear at doi:10.1107/S1399004715000826 > once it's online). At present, neither the structural quality checks in > commonly-used crystallography packages nor those run on deposition of a > structure to the PDB are flagging the presence of non-proline *cis *peptide > bonds. This has led to the presence of many erroneous *cis *bonds > creeping into the PDB - primarily in low-resolution structures as one would > expect, but I have identified clearly erroneous examples in structures with > resolutions as high as 1.3 Angstroms. From my analysis, I estimate that a > few thousand structures have been affected to some extent, with the worst > cases having as high as 3% of their peptide bonds in *cis*. Particularly > if you have published anything >2.5 Angstroms in the past few years, may I > gently suggest that you make a quick double-check of your deposited > structures? This can be done quickly and simply in Coot > (Extensions-Modelling-Residues with Cis peptide bonds). > > > Best regards, > > > Tristan > > >
