Finding potential carbohydrate binding site on protein
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6 weeks ago
Hansen_869 ▴ 40

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!

binding Protein ligand carbohydrate • 380 views
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You could use InterProScan

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

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

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scroll down

enter image description here

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

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5 weeks ago
Hansen_869 ▴ 40

Any other alternatives?

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