pdb
Search the Protein Data Bank by query or PDB ID to retrieve macromolecular structure metadata and download structure files in mmCIF or PDB format.
Instructions
Access the Protein Data Bank (RCSB PDB) for macromolecular structure data.
SEARCH: Provide "query" to find structures (e.g., "kinase inhibitor", "hemoglobin"). GET: Provide "pdb_id" to retrieve entry metadata with optional detail sections. DOWNLOAD: Provide "pdb_id" + download=true to save the structure file and get the file path.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | Free-text search query to find PDB entries. Omit pdb_id when searching. | |
| pdb_id | No | PDB identifier (e.g., "1CRN", "4HHB"). Required for get/download. | |
| sections | No | Metadata sections: polymer_entities (chains and sequences), ligands (small molecules and ions), assembly (biological assembly), experiment (method, resolution), citation (publication). Use "all" for everything. Default: core summary only. | |
| download | No | Save the structure file to disk and return the file path. Only used with pdb_id. | |
| format | No | File format: "cif" (mmCIF, recommended, always available) or "pdb" (legacy format, may not exist for some entries). Only used with download=true. | cif |
| limit | No | Max search results | |
| offset | No | Search result offset |