Glycan connectivity issues in output

HADDOCK
1

I have been using HADDOCK to dock glycans to proteins and I have noticed that you do not have a GalNAc option for when i am preparing the glycans for HADDOCK. I chanced my arm and see if the NAG label would work seeing as its still beta and they are isomers of each other ect. But HADDOCK then goes on to threat the glycan as monosaccharides instead. Is there any chance that implementing a GalNAC label?

2

The current list of supported glycan units is in:

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

And we might well be missing some connectivities (it is a complex landscape). What would be the official PDB code for GalNAC? And do you have an example PDB for the failing linkage?

3

I definitely sympathise with glycans being complex :laughing:.

I found NGA from the pdb 2D7R (resid 704) as a residue names for a GalNAc. Its essentially GlcNAC (NAG) however the O4 is axial instead of equatorial.

Glycan starts out like this.

glycan
glycan960×1016 63.9 KB

Output is as follows

glycant
glycant669×834 204 KB

1 Like
4

I found NGA from the pdb 2D7R (resid 704) as a residue names for a GalNAc. Its essentially GlcNAC (NAG) however the O4 is axial instead of equatorial.

Thanks - we will see what we can do…

As for the linkage issue, which exact linkage is missing (that’s the reason it is broken into two pieces).
I.e. what are the two glycans around that linkage and how are they linked?

5

I think its because its a beta 1-4 linkage. So when the system builds it into a GlcNAc, O4 is in the wrong position (equatorial instead of axial) for a bond to occur so it is not made.

6

Please send via email the PDB files of your glycan

7

Did that send ?

8

Got it - thanks