Dear Goran et al., when building O-linked glycans one should keep in mind that in contrast to N-glycans there is no single core structure in O-glycans, but a variety of different structures exist. Therefore, the NAG-SER linkage might be correct (if it is an O-GlcNAc modification, which is usually used as a molecular switch in a similar way as phosphorylation, see https://www.ncbi.nlm.nih.gov/books/NBK453063/ ), but it might be incorrect if it is a different kind of O-glycan, such as mucin-type O-glycan (starting with A2G, see https://www.ncbi.nlm.nih.gov/books/NBK453030/ ), O-mannosylation (starting with MAN, see e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500819/ ), a proteoglycan linker (starting with XYP, see https://www.ncbi.nlm.nih.gov/books/NBK453033/ ), or even one of some rare types of O-glycans (see https://www.ncbi.nlm.nih.gov/books/NBK453017/ ). This list might not be complete, as O-glycans are not my core expertise. It is probably not possible to identify the O-glycan type in the electron density, but it might help to check the literature if something is known on the type of O-glycan at that position of your protein, so that you can model the correct residue, or at least the most likely one, into your electron density.
Best regards, Thomas ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
