bond is
made the wrong way around.
Best regards,
Tristan
From: Tristan Croll
Sent: Tuesday, 17 February 2015 6:13 AM
To: wouter.t...@radboudumc.nl; CCP4 bulletin board
Subject: Re: [ccp4bb] Cis-peptide bond checking
Dear Wouter,
That does sound like a useful t
josea.cuesta.se...@carlsberglab.dk<mailto:josea.cuesta.se...@carlsberglab.dk>
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tristan
Croll
Sent: Monday, February 16, 2015 9:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Cis-peptide
To add to my rather spotty coverage of the literature on this subject:
- M. S. Weiss, H. J. Metzner & R. Hilgenfeld (1998). Two non-proline cis
peptide bonds may be important for factor XIII function. FEBS Lett. 423, 291-296.
- M. S. Weiss, A. Jabs & R. Hilgenfeld (1998). Peptide bonds revisite
c.nl
Sent: Monday, 16 February 2015 9:55 PM
To: Tristan Croll; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Cis-peptide bond checking
Dear Tristan,
Thank you for your post of earlier today regarding the problem of cis and trans
peptide planes in the PDB. We also realised this problem a while ago and
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" wrote:
> Dear all,
>
>
> My apologies for the spam-l
;mailto:CCP4BB@JISCMAIL.AC.UK>
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 be
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
bject: Re: [ccp4bb] Cis-peptide bond checking
Dear Tristan,
Thank you for your post of earlier today regarding the problem of cis and trans
peptide planes in the PDB. We also realised this problem a while ago and an
article describing this problem and a solution is presently under review at
Acta
Dear Tristan,
Thank you for your post of earlier today regarding the problem of cis and trans
peptide planes in the PDB. We also realised this problem a while ago and an
article describing this problem and a solution is presently under review at
Acta Cryst. D. After analysis of the PDB we can s
IL.AC.UK
Subject: RE: [ccp4bb] Cis-peptide bond checking
HmmCISPEP records are provided...
CISPEP 1 GLY A 63LEU A 64 0 1.59
CISPEP 2 LEU A 69PRO A 70 0 -14.05
CISPEP 3 PRO A 70PRO A 71 0-2.41
CISPEP 4 ASP A 1
be parsed/checked..
..but then again, who does?
https://www.youtube.com/watch?v=bAZqE2DnxUI
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tristan Croll
Sent: Montag, 16. Februar 2015 10:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Cis-peptide bond
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 che
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