show location of amino acid corresponding to SNP in a PDB model

Question

[theoharis]

I would like to show the location of an amino acid corresponding to a SNP in a PDB model. This is only for visualisation purposes.

[Ram]

As always, please mention what you have tried and where exactly you're facing a problem. Please read Ten Simple Rules for Getting Help from Online Scientific Communities.

[theoharis]

What I've tried is searching on this forum and general search engines. Ive been unable to find any mention of being able to go from a SNP rs number (provided its in a coding region) to viewing the location of the corresponding amino acid in the context of an existing PDB model. This is not for the purpose of predicting a change in the 3D structure but simple to show where in the protein the SNP maps to.

[Ram]

There will be no ready-made solution to get from point A to point B. The way these problems are solved is to find intermediate points/partial solutions and put these together in a reproducible manner.

You can get HGVS p. notation from the rs ID, which will give you a protein identifier and the residue change. From there, you can get to its UniProt/PDB identifier and use that in something like pymol to pick the appropriate residue and color it as you wish.

[Joe]

If you have a PDB of the protein, and you know the position of the substitution, it’s easy enough to colour residues differently etc.

There is not automatic tool for this that I know of however, so can you please clarify what it is you’re looking for? (A guide? A tool? Etc). Please also show us anything you’ve already attempted.

Here’s a previous guide for labelling residues: Label protein strucuture residues in Chimera

You can use chimeras sequence browser or the residue number nomenclature to make specific changes.

Answer 1

[Emily]

We have this in Ensembl. Search for the variant, then go to 3D protein model. For example rs699 in AGT.

[theoharis]

that's great - thanks