Protein Structure · RCSB Protein Data Bank
PDB Structure Fetch
Retrieves experimentally determined protein coordinates and metadata for any PDB entry.
What PDB Structure Fetch is
PDB Structure Fetch is a structure retrieval tool developed by the RCSB Protein Data Bank. It provides access to approximately 230,000 experimentally solved structures, offering researchers verified atomic coordinates alongside provenance records.
The tool supplies all-atom coordinate files in standard PDB format together with essential experimental context, including determination method, resolution, organism, deposition date, and bound ligands. These records allow scientists to benchmark computational models against experimental data or initiate molecular docking workflows from observed binding poses.
Key facts
- Version
- 1.0
- Task
- Structure retrieval
- Database size
- Roughly 230,000 experimentally solved structures
- Input format
- PDB ID (accession)
- Output format
- PDB structure coordinates and tabular metadata
- Hardware requirement
- CPU
What you can use it for
- Validation of structural predictions
- Inspect and compare predicted 3D models against experimentally determined all-atom coordinates.
- Seeding molecular docking
- Extract observed crystal structures and bound ligand coordinates to serve as starting geometries for docking calculations.
- Metadata and provenance extraction
- Retrieve experimental details for an accession, including structural resolution, determination method, host organism, and deposition date.
Run it here
No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.
Run this model
PDB Structure Fetch
Strengths and limits
Good at
- Provides all-atom coordinates together with comprehensive experimental provenance and bound ligand details.
- Accesses a library of roughly 230,000 experimentally determined structures.
- Executes on CPU hardware without requiring graphical processing units.
Watch out for
- Requires a known PDB accession code as input.
- Restricted to existing macromolecular structures catalogued within the repository.
Inputs and outputs
You provide
PDB ID
Four-character RCSB PDB identifier.
You get back
All-atom coordinates in PDB format, viewable and downloadable.
Method, resolution, organism, and deposition details.
Licence
Commercial use permitted · CC0
The CC0 licence allows use in commercial research and products.
Questions
Can I use PDB Structure Fetch commercially?
Commercial use permitted. The CC0 licence allows use in commercial research and products.
How do I run PDB Structure Fetch without installing anything?
Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers, typically in 600ms, and a run costs free. Visitors without an account get 1,000 credits a month.
What information does the output contain?
It provides downloadable all-atom coordinates in PDB format, alongside a metadata table specifying the experimental method, resolution, organism, deposition details, and bound ligands.
What input identifier is required?
A standard four-character PDB accession identifier is required to retrieve a structure.
Does this tool require GPU resources?
No, structure retrieval runs entirely on standard CPU resources.
Written from PDB Structure Fetch's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.