PDBe Download

Fetch PDB and mmCIF coordinate files from Protein Data Bank in Europe.

Input

Entry ID

Database

Output format

Output

Configure inputs to begin

Set options on the left, then click “Fetch downloads” — or start from an example.

1IVO

1CRN

4HHB

How to download PDBe records?

PDBe Download fetches Protein Data Bank in Europe structure files by PDB ID. It returns PDB and CIF coordinate files in the results panel along with experimental method and resolution metadata when available.

Use this tool when you want PDBe-hosted coordinate files for visualization, structure conversion, or comparison with other structure sources.

Input	Description
`Entry ID`	Four-character PDB ID. Examples: `1IVO`, `1CRN`, `4HHB`.

Setting	Description
`Database`	Opens the selected database download tool.
`Output format`	Return all files, PDB, or mmCIF.

Supported PDBe downloads

File	Format	Use
PDB	`.pdb`	Coordinate file in PDB format.
CIF	`.cif`	Coordinate file in mmCIF format.

Understanding the results

The results panel lists available PDBe files as remote downloads. The Details tab records the database, entry ID, record title, file label, format, source type, filename, and URL.

Filenames follow the pattern:

Text

pdbe-1IVO-pdb.pdb
pdbe-1IVO-cif.cif

For RCSB-hosted files and FASTA sequence downloads, use PDB Download. For extracting sequences from uploaded structures, use PDB to FASTA.

Common use cases

Download PDBe coordinate files for a known PDB ID.
Compare PDBe and RCSB file availability for the same entry.
Retrieve mmCIF files before structural analysis.
Open a downloaded file in PDB Viewer.

FAQ

Is PDBe different from RCSB PDB?

Both provide access to Protein Data Bank entries. PDBe is the European Protein Data Bank resource and offers its own APIs and entry pages.

Which format should I use?

Use CIF when possible for modern workflows. Use PDB when a downstream tool specifically requires the legacy PDB format.

Can I enter a UniProt accession?

The provider can search by UniProt accession in the database page, but this download tool is best used with a direct PDB ID.

Related tools

AlphaFold Database Download

Download AlphaFold DB predicted structures and confidence files by UniProt accession.

PDB Download

Download PDB, CIF, and FASTA files from RCSB PDB by 4-character structure ID.

BindingDB Download

Download BindingDB binding record files by BindingDB monomer ID.

InterPro Download

Download InterPro protein family and domain records as JSON by InterPro ID.

QuickGO Download

Download QuickGO Gene Ontology term records as JSON by GO ID.

UniProt Download

Download UniProt protein sequence records as FASTA and JSON by accession.

PDBFixer

PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.

PDB to CIF Converter

Convert Protein Data Bank files to Crystallographic Information File format

ChEBI Download

Download ChEBI chemical entity records as JSON by ChEBI ID.

ChEMBL Download

Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.