Question: show location of amino acid corresponding to SNP in a PDB model
gravatar for theoharis
11 months ago by
theoharis20 wrote:

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.

snp pdb • 300 views
ADD COMMENTlink modified 9 months ago by Emily_Ensembl21k • written 11 months ago by theoharis20

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.

ADD REPLYlink written 11 months ago by RamRS27k

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by theoharis20

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.

ADD REPLYlink written 11 months ago by RamRS27k

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.

ADD REPLYlink written 11 months ago by Joe17k
gravatar for Emily_Ensembl
9 months ago by
Emily_Ensembl21k wrote:

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

ADD COMMENTlink written 9 months ago by Emily_Ensembl21k

that's great - thanks

ADD REPLYlink written 7 months ago by theoharis20
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