Carbohydrate not attached to ASN residue during docking

HADDOCK
,
1

I have a BGLCNA carbohydrate that is attached to my protein through a N-linked glycosylation (to asparagine). It originally shows up in the PDB file as BGLC, which caused errors, so I changed it to GLC, and the job ran fine. I got good results, but I realized that the carbohydrate had drifted a few angstroms away in the docked poses. I realized that HADDOCK did not recognize the N-linkage. I was wondering if anyone knows a way to create that bond manually. I wanted to create a restraint but since the carbohydrate is a HETATM, I don’t think I can specify the carbon in the sugar molecule.

I was able to just build the bond back while preparing the system for MD simulations, but since the covalent bond is now 4 angstrom, I’m not sure if this will be corrected during minimization/equilibration.

Any advice is appreciated.

2

This is strange as this should be supported.
Could you share your input PDB?

3

Hi I found a support email from another post (haddock.support@gmail.com). I sent my PDB structure there.

4

Hi Norman

I took a look at your glycan. First you seem to need NDG instead of GLC since it is a N-acetylated one.
See: HADDOCK Web Server - Settings

I modified accordingly the PDB file and run a refinement server test.

All looks good and the glycan is connected to ASN (see the direct email you got with the files attached).