How To Retrieve The Rna Type From A Pdb File?

Question

[Noam N. Kremen]

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?

Answer 1

[Neilfws]

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...)

[Noam N. Kremen]

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).

[Vladimir Chupakhin]

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

[Neilfws]

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

[Vladimir Chupakhin]

..that are not always correct.