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How To Retrieve The Rna Type From A Pdb File?

I have a large collection of PDB files, each containing the structure of a protein in complex with an RNA molecule. I would like to find out (without going by hand through each PDB) the type of the RNA molecule (tRNA, mRNA, rRNA). Is there any program/web service that can help me achieve this?

rna pdb
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updated by Eugene F. Baulin • Eugene F. Baulin • written by Noam N. Kremen • Noam N. Kremen

2 answers

One way to do this would be to use PDBML XML files, rather than PDB format. These contain the tag PDBx:pdbx_description, which describes each type of molecule in the structure.

For example, if we search the PDB for molecules containing protein + RNA (using the advanced search facility), choose 3J13, download the XML file and:

grep "PDBx:pdbx_description" 3J13.xml

We see (just showing the first 3 lines):

     <PDBx:pdbx_description>16S ribosomal RNA</PDBx:pdbx_description>
     <PDBx:pdbx_description>mRNA</PDBx:pdbx_description>
     <PDBx:pdbx_description>P site tRNA</PDBx:pdbx_description>

You can parse the XML files in the language of your choice (Ruby, Python, Perl...)

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written by Neilfws Neilfws

Thanks, that pointed me in the right direction. Filtering on polyribonucleotide PDBX:type is needed first to get the chain id(s) of the RNA(s).

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written by Noam N. Kremen • Noam N. Kremen

I don't think that description give fully correct details, esp. for old records. So, you should be careful.

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written by Vladimir Chupakhin Vladimir Chupakhin

Well it's only as good as the PDB curators, obviously.

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written by Neilfws Neilfws

Not ideal solutions, but here:

1) Rfam-PDB mappings: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.pdb.gz

2) Representative sets of RNA structures: https://rna.bgsu.edu/rna3dhub/nrlist/release/rna/3.374

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written by Eugene F. Baulin • Eugene F. Baulin

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