Pdbe Ligands Tools

Configuration File: pdbe_ligands_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the pdbe_ligands_tools.json configuration file.

Available Tools

PDBe_get_residue_listing (Type: PDBeLigandsTool)

Get per-residue information for a PDB structure, optionally filtered by chain. Returns residue nu…

PDBe_get_residue_listing tool specification

Tool Information:

  • Name: PDBe_get_residue_listing

  • Type: PDBeLigandsTool

  • Description: Get per-residue information for a PDB structure, optionally filtered by chain. Returns residue numbers (both PDB sequential and author-assigned), residue names (3-letter amino acid codes), and observed ratio (fraction of models where this residue has electron density). Useful for analyzing protein chain composition, identifying disordered/missing regions (observed_ratio < 1.0), or mapping between PDB and author numbering schemes. Example: ‘4hhb’ chain A returns 141 residues (alpha globin) all with 1.0 observed ratio; ‘3ert’ chain A returns 261 residues (estrogen receptor) starting at author residue 294.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘4hhb’, ‘3ert’, ‘1tup’, ‘6lu7’. Case-insensitive.

  • chain_id ([‘string’, ‘null’]) (optional) Optional chain ID to filter (e.g., ‘A’, ‘B’). If not provided, all chains are returned.

Example Usage:

query = {
    "name": "PDBe_get_residue_listing",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

PDBe_get_structure_ligands (Type: PDBeLigandsTool)

Get all ligands (drug-like molecules, cofactors, ions) bound in a PDB crystal structure. Returns …

PDBe_get_structure_ligands tool specification

Tool Information:

  • Name: PDBe_get_structure_ligands

  • Type: PDBeLigandsTool

  • Description: Get all ligands (drug-like molecules, cofactors, ions) bound in a PDB crystal structure. Returns chemical component IDs, names, molecular weights, chain assignments, and drug-likeness annotations with interacting protein entity information. Essential for studying protein-ligand interactions, identifying bound drugs/inhibitors, or analyzing binding site occupancy. Example: ‘4hhb’ returns 6 HEM (heme) ligands bound to hemoglobin alpha and beta chains; ‘3ert’ returns 4-hydroxytamoxifen (OHT, 387 Da) bound to estrogen receptor alpha; ‘1m17’ returns erlotinib bound to EGFR kinase domain.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘4hhb’ (hemoglobin), ‘3ert’ (estrogen receptor + tamoxifen), ‘1m17’ (EGFR + erlotinib), ‘6lu7’ (SARS-CoV-2 main protease + inhibitor). Case-insensitive.

Example Usage:

query = {
    "name": "PDBe_get_structure_ligands",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)