NAGs of protein completely moved away after docking. How to solve this problem?

HADDOCK
1

I am using the SARS-CoV-2 RBD domain and human ACE2 (PDB ID:6LZG) receptor in HADDOCK server to predict top model and compare with existing PDB to validate HADDOCK method.

By giving known active site residues of RBD and ACE2 from PDB.

Note: There is a presence of 3 glycans attached on ACE2 protein and 1 glycan on RBD protein.

Glycan attached to nitrogen atom of Asparagine(Asn-N) residue by glycosidic bond (type of covalent bond).

After protein-protein docking, the bond breaks between glycan and Asn residue and all NAGs moved away from protein.

How to restraint to keep bond without breaking after protein-protein docking?

Why is there a break in covalent bond even though it is very strong?

2

The server does not support glycosylated proteins (yet). I will accept the glycans, but no covalent bond is created. So you will have to define some distance restraints to keep the glycans in place.

But we should have soon support for glycosylated ASN!

3

Glad to announce that as of today the HADDOCK2.4 server is supporting glycosylated proteins. The list of supported glycans can be found at:

https://wenmr.science.uu.nl/haddock2.4/library

4

Thank you so much for the information. I will try it immediately.