pdb
Search the Protein Data Bank for macromolecular structures, retrieve entry metadata, and download structure files for analysis.
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 |
|---|---|---|---|
| limit | No | Max search results | |
| query | No | Free-text search query to find PDB entries. Omit pdb_id when searching. | |
| 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 |
| offset | No | Search result offset | |
| pdb_id | No | PDB identifier (e.g., "1CRN", "4HHB"). Required for get/download. | |
| download | No | Save the structure file to disk and return the file path. Only used with pdb_id. | |
| 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. |