PDB to FASTA converter

Convert PDB structure files to FASTA format. Extract protein sequences from 3D structures. Upload a PDB file or fetch from the Protein Data Bank.

Input (PDB format)

PDB

Output (FASTA format)

FASTA

Why convert PDB to FASTA?

PDB files contain detailed 3D structural information, but sometimes you only need the amino acid sequences. Our converter extracts the sequence data while preserving chain information and annotations.

PDB files store 3D coordinates of every atom in a protein structure, along with experimental details and metadata. They're essential for structural analysis but can be large and complex.

FASTA files contain just the amino acid sequence in a simple text format. They're perfect for sequence analysis, alignments, and when you don't need structural information.

How to use the PDB to FASTA converter

  1. Select your PDB file from your computer or paste PDB text directly into the input field. You can also drag and drop your file into the input field.
  2. Choose whether to include all chains or select specific ones. Set custom header formats if needed.
  3. Click convert and download your FASTA file instantly. Results appear immediately for small files.

Example conversion

Input PDB snippet:

ATOM      1  N   MET A   1      20.154  16.967  14.812  1.00 25.00           N
ATOM      2  CA  MET A   1      19.030  16.654  15.721  1.00 25.00           C
ATOM      3  C   MET A   1      17.713  16.496  14.962  1.00 25.00           C
ATOM      4  O   MET A   1      17.000  15.500  14.500  1.00 25.00           O
ATOM      5  CB  MET A   1      18.900  15.500  16.500  1.00 25.00           C
ATOM      6  CG  MET A   1      18.000  14.500  17.200  1.00 25.00           C
ATOM      7  SD  MET A   1      16.500  14.500  18.500  1.00 25.00           S
ATOM      8  CE  MET A   1      15.500  13.500  19.200  1.00 25.00           C
ATOM      9  NZ  MET A   1      14.500  13.500  20.500  1.00 25.00           N
...

Output FASTA:

>1ABC_A Crystal structure of example protein, Chain A
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASE
DLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH

Frequently asked questions

What if my PDB file has multiple chains?

Our converter handles multi-chain proteins automatically. Each chain becomes a separate FASTA entry with clear chain identifiers in the header.

Do you preserve the original sequence numbering?

The FASTA output shows the actual amino acid sequence. Original PDB numbering is included in the header metadata for reference.

Can I convert modified amino acids?

Yes, we handle standard modifications and will note non-standard residues in the output. Complex modifications are converted to their closest standard amino acid.

What's the file size limit?

Our free tool handles files up to 50MB. For larger batch processing, check out our premium dashboard with enhanced features.

Is my data secure?

Absolutely. Files are processed locally in your browser when possible, and server-processed files are automatically deleted after conversion.

Convert PDB files to FASTA format quickly and accurately. Perfect for researchers, students, and bioinformatics professionals who need clean sequence data from structural files.

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