Hi Ed, That is exactly the point the validation tools in WHAT_CHECK, to detect cis-peptides if missed. I think these are more likely to have biological implications than the transpeptides modeled as cis. Most of those cases are part of poorly modeled regions with difficult to interpret density. Tristan raised an important point, we should be suspicious of cispeptides, especially at low resolution, and check the evidence. They are less common so they do need extra evidence. However, if the map is clear we shouldn't be paranoid. This should always be part of the model building and validation process, but it is clear from the PDB that not everyone is equally skilled and diligent.
Cheers, Robbie Sent with my Windows Phone ________________________________ Van: Edward A. Berry<mailto:[email protected]> Verzonden: 16-2-2015 18:32 Aan: [email protected]<mailto:[email protected]> Onderwerp: Re: [ccp4bb] Cis-peptide bond checking However it is important to note that there are real non-proline cis peptides in high-resolution structures, and to not throw out these babies with the bathwater! In fact I think they are probably under-represented because people are hesitant to build a non-pro cis peptide even when the density favors it, unless it is absolutely clear! Examples: 2BS2 1.78 Asp A398 trans, should be cis. http://sb20.lbl.gov/SQR/cis-asp398.gif 3cx5 1.8 Ser C223 trans, should be cis, corrected in 4PD4 1NEK 2.6 Ser-A393 trans, should be cis, corrected in 2WDQ Stewart, D. E., Sarkar, A., and Wampler, J. E. (1990) J. Mol. Biol. 214, 253–260 D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations, J. Mol. Biol. 294 (1999) 271–288. eab On 02/16/2015 04:58 AM, Tristan Croll 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 > >
