Get comprehensive information about a PDB entry.

Args: pdb_id: The 4-character PDB identifier (e.g., '1ABC', '7BQY')

Returns: JSON string containing entry information including: - Structure title and description - Experimental method (X-ray, NMR, Cryo-EM, etc.) - Resolution - Deposition and release dates - Authors and citation information - Organism source

Get information about a polymer entity (protein, DNA, RNA) within a PDB entry.

Args: pdb_id: The 4-character PDB identifier (e.g., '1ABC') entity_id: The entity number within the structure (default: '1')

Returns: JSON string containing polymer entity information including: - Molecule name and description - Sequence information - Molecular weight - Entity type (polypeptide, DNA, RNA, etc.) - Source organism

Download a structure file from RCSB PDB.

Args: pdb_id: The 4-character PDB identifier (e.g., '1ABC') file_format: Format to download. Options: - 'pdb': PDB format (default) - 'cif': mmCIF format - 'xml': PDBML/XML format - 'pdb.gz': Compressed PDB - 'cif.gz': Compressed mmCIF - 'xml.gz': Compressed XML output_dir: Directory to save the file (optional, defaults to current directory) filename: Custom filename (optional, uses PDB ID + extension by default)

Returns: JSON string with download status and file path

Make a custom query to the RCSB Data API.

This is an advanced tool for accessing any RCSB Data API endpoint directly.

Args: endpoint: API endpoint path (e.g., 'assembly/1ABC-1', 'uniprot/P12345') params: Optional JSON string of query parameters (e.g., '{"format": "json"}')

Common endpoints: - entry/{pdb_id}: Entry-level information - polymer_entity/{pdb_id}{entity_id}: Polymer entity info - assembly/{pdb_id}-{assembly_id}: Biological assembly info - nonpolymer_entity/{pdb_id}{entity_id}: Small molecule/ligand info - uniprot/{uniprot_id}: UniProt cross-reference

Returns: JSON string containing the API response

Get information about how to search for PDB entries by organism.

This tool provides guidance on using the RCSB search API to find structures from specific organisms.

Args: organism: Organism name (e.g., 'Homo sapiens', 'E. coli')

Returns: Instructions and example queries for searching by organism