I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.

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    – Ram RS
    Sep 18, 2019 at 18:19

1 Answer 1


There may also be a misunderstanding, from your previous post. To reiterate, I don't use Ensembl, which is the source of your gene names.

On Genbank there is an entire "Structural" database for every structure that is on PDB. When Genbank hold the protein sequence that was used to generate the structure Genbank only use PDB codes. For example "5LBV_A" is both a PDB code and a Genbank code. So this means PDB entry 5LBV chain A. Thus its easy to download the crystal because you simply ask PDB for 5LBV. To prove it,

efetch -db protein -format gpc -id "5LBV_A" | xtract -pattern INSDSeq -group INSDSeq -element INSDSeq_sequence

OUT ircigvsnrdfvegmsggtwvdvvlehggcvtvmaqdkptvdielvtttvsnmaevrsycyeasisdmasdsrcptqgeayldkqsdtqyvckrtlvdrgwgngcglfgkgslvtcakfacskkmtgksiqpenleyrimlsvhgsqhsgmivndtghetdenrakveitpnspraeatlggfgslgldceprtgldfsdlyyltmnnkhwlvhkewfhdiplpwhagadtgtphwnnkealvefkdahakrqtvvvlgsqegavhtalagaleaemdgakgrlssghlkcrlkmdklrlkgvsyslctaaftftkipaetlhgtvtvevqyagtdgpckvpaqmavdmqtltpvgrlitanpvitestenskmmleldppfgdsyivigvgekkithhwhrsgstiggpfeddddkagwshpqfekgggsgggsgggswshpqfek

What I cannot easily do, is go from a generic NCBI Genbank protein code to PDB code.

However, PDB uses Uniprot codes for proteins, so you may be able to use a Uniprot code to get hold of the PDB code, or Ensembl codes may, like Genbank, use PDB accessions.

So in summary perhaps you need to give more detail?


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