PDB to FASTA converter

What is PDB to FASTA converter?

PDB to FASTA converter extracts protein and nucleic acid sequences from structure files. PDB files contain 3D atomic coordinates, but many bioinformatics tools require only the sequence in FASTA format. This tool reads the structural data and outputs clean, properly formatted sequences.

The converter handles multi-chain complexes, DNA and RNA chains, and structures with missing or modified residues. You can fetch structures directly from the RCSB Protein Data Bank using a 4-character PDB ID, or upload your own files.

For visualizing PDB structures before conversion, use the PDB Viewer. If your structure has issues like missing atoms or non-standard residues, the PDB Fixer can clean it up first.

How to convert PDB to FASTA?

PDB files store amino acid information in ATOM and HETATM records. Each record contains a three-letter residue code (like ALA for alanine, GLY for glycine) along with the chain identifier and residue number.

The conversion reads these records in sequence order, extracts the residue codes for each chain, and maps the three-letter codes to one-letter amino acid codes using the IUPAC convention.

By default the tool reports the observed sequence, meaning only residues that have 3D coordinates. When a structure has disordered loops or unresolved termini, those residues are absent from the coordinates. To get the complete sequence that was present in the sample, switch the sequence source to the deposited SEQRES records.

The conversion follows the standard amino acid abbreviations:

Inputs and settings

Sequence

Chain selection

Chain filtering

Chain filtering is off by default, so every chain is kept. Turn it on to refine your output when working with large complexes or structures with many small peptide fragments.

Missing and modified residues

Output formatting

Understanding the results

The output is standard FASTA format with one or more sequences. Each sequence begins with a header line starting with >, followed by the amino acid sequence.

>1HTM_A
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVV
HSLAKWKRQQIAAALEHHHHHH
>1HTM_B
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVV
HSLAKWKRQQIAAALEHHHHHH

The extracted sequences can be used directly with sequence analysis tools like Amino Acid Composition, Protein Parameters, or structure prediction tools like ESMFold and Boltz-2.

Common use cases

Extracting sequences from experimental structures is often the first step in computational workflows. You might need the sequence to:

• Search for homologs using BLAST or similar tools
• Predict properties like isoelectric point or molecular weight
• Use as input for structure prediction to compare with the experimental structure
• Design primers for cloning or mutagenesis