I am working on docking a glycoprotein with four branched glycan chains linked to protein ASN residues. The docking completes successfully however in the output structures the terminal residue of the glycan, SIA, has become unbonded and wandered away from the glycan chains. In my pre-docking structures the SIAs are in place and bonded. I read that Haddock has recently started supporting glycans and the structures look good aside from this issue; any advice on how to keep the SIA bound to the previous GAL would be appreciated.
Thank you very much,
I assume you have been using the 2.4 server?
There are many glycans and many linkages possible. We might well be missing some combinations…
What is the linkage type for SIA and to which unit is it linked to?
I am on the 2.4 server. The SIA is linked to GAL by an alpha 6 linkage. The structure template is pasted below, with SIA as the terminal red diamond. I hope this helps and thank you for your quick response!
Could you please share with us the input PDB file (or only the peptide part containing that glycan)?
Certainly. I’ve attached the input pdb. There are 4 glycans linked to ASN 143, 164, 174 and 234.
b2glycan_10nsequili_chainrenum.pdb (474 KB)
We (should) have fixed the problem (2-6 and 2-3 SIA-GAL linkages were added).
Can you give it another try?
I have tested it, the problem is fixed! Adding glycan support has helped a lot for my project, thank you.
Perfect! Glad to hear that.