Finding potential carbohydrate binding site on protein

Question

[Hansen_869]

I have a protein with a known sequence and alphafold structure (so just a model). I know that the protein is binding some sugar molecule. Due to financial limitations, I am unable to peform a ligand binding assay. Is there any way to predict or atleast roughly estimate where on the protein the binding site is, and which sugar molecule it is binding?

Ideally, I need to find a protein with known structure that resembles my alphafold structure and use that as a reference when finding binding site.

I thought about finding lots of sugar binding proteins and see if my structure resembles some of them.

What are your suggestions?

Thanks!

[andres.firrincieli]

You could use InterProScan

Here is an example of a protein with a carbohydrate-binding module CBM49 in the region 501- 583

[Hansen_869]

Thanks for your reply. However, I only get the name of the protein. No function or the like. Any other suggestions?

[andres.firrincieli]

scroll down

[Hansen_869]

I see that, but I mean for the protein I am looking at. There's no info of that kind. Any other suggestions?

Answer 1

[Hansen_869]

Any other alternatives?