extract fasta sequences from PDB file by using perl script

Question

[skjobs1234]

I would like to extract one letter amino acid code from the PDB coordinate file.

[Kevin Blighe]

It would be helpful to paste an example PDB co-ordinate file. I'm not a Perl programmer, so, I won't provide an answer anyway, but it will help the other Perl programmers here.

[skjobs1234]

ATOM      1  N   MET A 183      14.367  14.409 -14.168  1.00 50.39           N  
ATOM      2  CA  MET A 183      14.811  14.674 -15.562  1.00 48.32           C  
ATOM      3  C   MET A 183      13.602  14.830 -16.511  1.00 43.21           C  
ATOM      4  O   MET A 183      13.525  14.177 -17.547  1.00 43.55           O  
ATOM      5  CB  MET A 183      15.718  13.527 -16.033  1.00 48.72           C  
ATOM      6  N   LEU A 184      12.672  15.708 -16.152  1.00 42.00           N  
ATOM      7  CA  LEU A 184      11.447  15.964 -16.970  1.00 39.32           C  
ATOM      8  C   LEU A 184      11.678  16.660 -18.321  1.00 41.97           C  
ATOM      9  O   LEU A 184      10.824  16.619 -19.224  1.00 39.74           O  
ATOM     10  CB  LEU A 184      10.478  16.835 -16.169  1.00 38.33           C  
ATOM     11  CG  LEU A 184       9.839  16.253 -14.920  1.00 36.74           C  
ATOM     12  CD1 LEU A 184       8.881  17.262 -14.332  1.00 38.09           C  
ATOM     13  CD2 LEU A 184       9.103  14.968 -15.262  1.00 35.13           C  
ATOM     14  N   LYS A 185      12.791  17.375 -18.435  1.00 42.50           N  
ATOM     15  CA  LYS A 185      13.161  18.016 -19.691  1.00 41.45           C  
ATOM     16  C   LYS A 185      13.722  16.983 -20.669  1.00 41.88           C  
ATOM     17  O   LYS A 185      13.747  17.251 -21.873  1.00 47.12           O  
ATOM     18  CB  LYS A 185      14.184  19.158 -19.455  1.00 40.64           C  
ATOM     19  N   LYS A 186      14.182  15.814 -20.201  1.00 37.88           N  
ATOM     20  CA  LYS A 186      14.726  14.837 -21.141  1.00 36.11           C  
ATOM     21  C   LYS A 186      13.577  14.319 -22.001  1.00 35.18           C  
ATOM     22  O   LYS A 186      12.478  13.996 -21.479  1.00 34.26           O  
ATOM     23  CB  LYS A 186      15.460  13.672 -20.470  1.00 36.66           C  
ATOM     24  N   LYS A 187      13.842  14.254 -23.298  1.00 33.43           N  
ATOM     25  CA  LYS A 187      12.881  13.836 -24.324  1.00 32.15           C  
ATOM     26  C   LYS A 187      12.824  12.313 -24.346  1.00 30.19           C  
ATOM     27  O   LYS A 187      13.387  11.676 -25.230  1.00 31.65           O  
ATOM     28  CB  LYS A 187      13.337  14.358 -25.694  1.00 34.18           C

[h.mon]

And the expected output is? I guess for this example is MLKKK, is that right? Or do you want MMMMMLLLLLLL...?

[Ram]

Why Perl? Usually, when we're addressing a bioinformatics problem, we look at the best tool for the job, not how to do something limiting ourselves to just one specific tool.

[natasha.sernova]

I found one more way.

See this site below:

http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/

Insert a structure ID and/or the author surname:

http://www.ebi.ac.uk/pdbe/entry/pdb/1aa0/

Fetch sequence in the left bottom corner of the page:

VSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVLLSTFL

OR

Quick links (right upper corner)

• 1aa0 overview

http://www.ebi.ac.uk/pdbe/entry/pdb/1aa0/protein/1

Macromolecules:

pdb|1aa0|A VSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVLLSTFL

There are several ways to find a sequence.

Answer 1

[h.mon]

This can get you started, you can then modify it to suit your needs. Save it as get_pdb_aa.pl, and run with get_pdb_aa.pl < file.pdb > out.txt. This will output MMMMMLLLLLLLLKKKKKKKKKKKKKKK for the example you provided.

#!/usr/bin/env perl

use warnings;
use strict;

my %aa_table = (
ala => 'A',arg => 'R',asn => 'N',asp => 'D',
asx => 'B',cys => 'C',glu => 'E',gln => 'Q',
glx => 'Z',gly => 'G',his => 'H',ile => 'I',
leu => 'L',lys => 'K',met => 'M',phe => 'F',
pro => 'P',ser => 'S',thr => 'T',trp => 'W',
tyr => 'Y',val => 'V',
);

foreach my $line ( <STDIN> ) {
    my ($v1, $aa, $v3) = unpack 'A17A3A60', $line;
    print "$aa_table{ lc($aa) }";
}

[rolanda763]

can you tell me more, how unpack works in this case? and how it would be if the pdb file lines looks like this: ATOM 1 N N . MET A 1 1 ? 36.644 -24.949 8.853 1.00 29.12 ? 1 MET A N 1 ????????