pdb
Search, retrieve, and download macromolecular structures from the Protein Data Bank using queries or PDB IDs.
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. |