Gene Name from PDB id
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3.1 years ago

How do i retrieve the gene names from a list of PDB id's ? say for example: MAPK3 from 2ZOQ

I would like to do it all at once

gene • 1.5k views
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3.1 years ago
goodez ▴ 490

Check out Ensembl's BioMart: https://www.ensembl.org/biomart

Once you are there, choose "Ensembl Genes 93" as the database, then choose "Human Genes" as the dataset (assuming this is human).

Then go over to filters on the left side and expand the Gene section. Check the box that says "Input external references ID list" and select from the dropdown menu "PDB ID(s)". This is where you input your list of PDB IDs

Now go back to the left side and click Attributes. Expand the Gene section and select "Gene name".

Finally on the top left choose Results and you can choose how to output this table.

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3.1 years ago
GenoMax 107k

If you use PDB REST interface.

<molDescription><structureId id="2ZOQ"><polymer entityNr="1" length="382" type="protein" weight="43527.8"><chain id="A"/><chain id="B"/><Taxonomy name="Homo sapiens" id="9606"/><synonym name="Extracellular signal-regulated kinase 1, ERK-1, Insulin-stimulated MAP2 kinase, MAP kinase 1, MAPK 1, p44-ERK1, ERT2, p44-MAPK, Microtubule-associated protein 2 kinase"/><macroMolecule name="Mitogen-activated protein kinase 3"><accession id="P27361"/></macroMolecule><polymerDescription description="Mitogen-activated protein kinase 3"/><enzClass ec="2.7.11.24"/></polymer></structureId></molDescription>

Using NCBI's unix utils

$ esearch -db protein -query "2ZOQ" | esummary | xtract -pattern DocumentSummary -element Title

RecName: Full=Mitogen-activated protein kinase 3; Short=MAP kinase 3; Short=MAPK 3; AltName: Full=ERT2; AltName: Full=Extracellular signal-regulated kinase 1; Short=ERK-1; AltName: Full=Insulin-stimulated MAP2 kinase; AltName: Full=MAP kinase isoform p44; Short=p44-MAPK; AltName: Full=Microtubule-associated protein 2 kinase; AltName: Full=p44-ERK1
Chain B, Structural Dissection Of Human Mitogen-Activated Kinase Erk1
Chain A, Structural Dissection Of Human Mitogen-Activated Kinase Erk1
44kDa protein kinase [Homo sapiens]
protein serine/threonine kinase [Homo sapiens]
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This is cool, but seems a bit overcomplicated to do this for a whole list of PDB IDs. If he just wants to extract gene names, BioMart only requires a few clicks

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Some people will not want to use a GUI tool (though biomart could still be used for this) so there’s no harm in approaching it this way either.

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