PDB structure (declared sequence) to FASTA converter

Convert a PDB structure (declared sequence) sequence file to FASTA.

Convert from Convert to Choose your sequence file

Maximum file size: 50 MB. The file is checked before conversion.

PDB structure (declared sequence) → FASTA

This reads the full sequence declared by the structure record, which may differ from observed coordinates.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.pdb-seqres", "pdb-seqres",
                      "output.fasta", "fasta")
print("Converted %i records" % count)

Sample input file: PDB structure (declared sequence)

Copy this example into a file, or download it, to try a PDB structure (declared sequence) conversion.

HEADER    VIRAL PROTEIN                           27-MAR-98   1A8O              
TITLE     HIV CAPSID C-TERMINAL DOMAIN                                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HIV CAPSID;                                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 151 - 231;                     
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SEQRES   1 A   70  MSE ASP ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP          
SEQRES   2 A   70  TYR VAL ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN          
END

Download sample (sample.pdb, 814 bytes)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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