[Inquiry to retrieve the SEQRES from PDB file] about biopython HOT 4 CLOSED

PDB code 2lwk can be viewed at https://files.rcsb.org/view/2LWK.pdb and contains:

HEADER    RNA                                     01-AUG-12   2LWK              
TITLE     SOLUTION STRUCTURE OF SMALL MOLECULE-INFLUENZA RNA COMPLEX            
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RNA (32-MER);                                              
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES 
...
DBREF  2LWK A    1    32  PDB    2LWK     2LWK             1     32             
SEQRES   1 A   32    G   A   G   U   A   G   A   A   A   C   A   A   G          
SEQRES   2 A   32    G   C   U   U   C   G   G   C   C   U   G   C   U          
SEQRES   3 A   32    U   U   U   G   C   U                                      
HET    0EC  A 101      40               
...

Confirming behaviour:

$ wget https://files.rcsb.org/view/2LWK.pdb
$ python -c "import sys; from Bio import SeqIO; SeqIO.convert('2LWK.pdb','pdb-seqres', sys.stdout, 'fasta')"
>2LWK:A PDB:2LWK 2LWK
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

The SEQRES lines are not residues, but nucleotides. As per the COMPND lines, this is an RNA chain, not protein.

This is as documented, although perhaps an error or warning would help for non-protein chains:

    - pdb-seqres -  Reads a Protein Data Bank (PDB) file to determine the
      complete protein sequence as it appears in the header (no dependencies).

Closing as a duplicate of #3125.

from biopython.

Thank you for your clarification.

Indeed, I am seeking to retrieve the complete RNA sequence utilized in the experiment. Given that the structure consists of nucleotides and represents an RNA chain, I am interested in exploring if there is a method within Biopython or any alternative approach to obtain the complete RNA sequence from the PDB file.

Your guidance on how to accomplish this using Biopython or any other relevant tools would be greatly appreciated.

Thank you for your assistance.

from biopython.

Well you could parse the SEQRES lines from the header (via the PDB parser), either DIY code or you might consider extending the code here to handle DNA and RNA:

https://github.com/biopython/biopython/blob/biopython-183/Bio/SeqIO/PdbIO.py#L113

I think it should look at the COMPND lines to tell if a chain is expected to be protein, RNA or RNA...

Or, you can look at the 3D structure but that would be more complicated.

from biopython.

Closing as a duplicate of #3125 (I evidently clicked the wrong button last time)

from biopython.