PDBe Download

What is PDBe Download?

PDBe Download is a structure-file retrieval tool for records in Protein Data Bank in Europe, the European partner of the Worldwide Protein Data Bank. Given a PDB entry identifier, it retrieves the deposited atomic coordinates as legacy PDB or PDBx/mmCIF files from PDBe.

The PDB archive is a shared global resource, so the same structure may also be available from other wwPDB partners. PDBe Download is most useful when a workflow uses PDBe entry pages, PDBe APIs, or PDBe-hosted coordinate URLs and needs a direct, reproducible file retrieval step. It retrieves the archive record, not a predicted structure or a model prepared for a particular simulation or docking workflow.

How to use PDBe Download online

ProteinIQ retrieves a PDBe structure record from a four-character PDB ID, such as 1IVO, then returns downloadable PDB and mmCIF coordinate files in the selected format. Each result identifies the archive entry and the PDBe source URL, making it possible to keep the coordinate file connected to its public record.

Input and settings

An entry that has been removed, is not publicly released, or does not match a current PDBe record returns an entry-not-found message. Direct ID retrieval avoids ambiguity between structures with related titles, chains, or associated UniProt accessions.

Files returned

Both formats describe the same deposited entry but are not interchangeable at the syntax level. PDB is a fixed-column legacy format with constraints that can make it unsuitable for some larger or more complex structures. PDBx/mmCIF is the archival format designed to represent the full PDB data model, so it is the safer default when a downstream program accepts it.

Understanding the results

The Files panel contains one downloadable item per selected format. File names are normalized for the download while preserving the PDBe entry ID, for example:

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

Each file records its source URL and format. Follow the PDBe entry link to inspect the deposited structure's title, experimental method, resolution where applicable, validation, biological-assembly context, and primary citation.

Resolution should be read together with method, completeness, validation, and the scientific question. A lower value usually means finer experimental detail for diffraction or cryo-EM structures, but it does not by itself establish that every region, ligand placement, or biological assembly is reliable. PDBe's entry page remains the appropriate place to inspect that context before making a high-stakes structural interpretation.

Choosing a format for downstream work

Choose mmCIF when the next program supports it. It preserves a richer representation of the archive and avoids many PDB-format limits. Choose PDB only when a particular viewer, legacy script, or analysis program requires it.

For quick inspection of either coordinate file, open it in the PDB Viewer. To derive polymer sequences from a downloaded structure, use PDB to FASTA. The PDB Download tool is a better fit when the same workflow also needs the structure-associated FASTA file from RCSB PDB.

PDBe Download handles one known archive entry at a time. For a collection of structures, query-based discovery, bulk downloads, biological assemblies, validation reports, or other record types, use PDBe's own download service or API and retain the exact archive release and file selection in the analysis record.