In the monomer library, pyr-SER and pyr-THR links are defined for the O-glycosylation. A monomer should belong to the "pyranose" group in the library (or in a user-provided dictionary).
Best regards, Keitaro On Fri, 14 Jul 2023 at 09:22, Jon Agirre <000017a7df66b7b3-dmarc-requ...@jiscmail.ac.uk> wrote: > > To the best of my knowledge, there is no o-glycan equivalent of the Coot > glyco plugin. We (as in YSBL, York) are working with others to provide tools > to build all kinds of glycans, but there's nothing you can use at this point. > I would deal with it like I'd do with other modifications, get monomer, make > the link, repeat. Links are likely to be part of the CCP4 monomer library > already. Also, they are likely to be short-ish glycans, so hopefully the task > won't be too onerous. > One issue depending on the resolution is the identification of the > monosaccharides. But you can have a look at some of the many possibilities > here: > https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue > It might help to look at other o-glycosylated structures in the PDB. You can > now do pretty powerful searches on the PDB. Alternatively, I'm sure someone > in my team could provide a list of all o-glycans Privateer can detect in the > PDB. > Hope this helps, > Jon > > > On Fri, 14 Jul 2023 at 09:03, Jonas Emsley > <00008d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Dear All >> >> >> >> We have a crystal structure with O-glycans for the first time attached to a >> Ser and a Thr sidechain >> >> >> >> If anyone can recommend the procedure for adding these in coot and refining >> them in phenix /refmac that would be greatly appreciated >> >> >> >> All the best >> >> >> >> jonas >> >> >> >> >> >> >> >> ################################## >> Dr Jonas Emsley >> Professor of Macromolecular Crystallography, >> Nottingham Biodiscovery Institute >> School of Pharmacy, >> University of Nottingham, >> University Park, >> Nottingham. >> NG72RD >> Tel: +44 1158467092 >> Fax: +44 1158468002 >> email:jonas.ems...@nottingham.ac.uk >> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx >> >> https://orcid.org/0000-0002-8949-8030 >> >> >> >> >> >> >> >> >> >> >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please contact the sender and delete the email and >> attachment. >> >> Any views or opinions expressed by the author of this email do not >> necessarily reflect the views of the University of Nottingham. Email >> communications with the University of Nottingham may be monitored >> where permitted by law. >> >> >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > -- > Dr Jon Agirre > Royal Society University Research Fellow (assistant professor) > CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) > York Structural Biology Laboratory, Department of Chemistry > University of York, Heslington, YO10 5DD, York, UK > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
