Pdbe Sifts Tools

Configuration File: pdbe_sifts_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

PDBeSIFTS_get_all_structures (Type: PDBeSIFTSTool)

Get all PDB structures for a UniProt protein, grouped by PDB entry with chain details, from PDBe …

PDBeSIFTS_get_all_structures tool specification

Tool Information:

  • Name: PDBeSIFTS_get_all_structures

  • Type: PDBeSIFTSTool

  • Description: Get all PDB structures for a UniProt protein, grouped by PDB entry with chain details, from PDBe SIFTS. Unlike best_structures which returns a flat ranked list, this groups results by PDB ID showing all chains per structure, sorted by resolution. Useful for comprehensive structural coverage analysis. Example: P04637 (TP53) has structures across hundreds of unique PDB entries covering different domains and complexes.

Parameters:

  • uniprot_accession (string) (required) UniProt accession for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

Example Usage:

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

PDBeSIFTS_get_best_structures (Type: PDBeSIFTSTool)

Get the best available PDB structures for a UniProt protein, ranked by coverage and resolution fr…

PDBeSIFTS_get_best_structures tool specification

Tool Information:

  • Name: PDBeSIFTS_get_best_structures

  • Type: PDBeSIFTSTool

  • Description: Get the best available PDB structures for a UniProt protein, ranked by coverage and resolution from PDBe SIFTS. Returns PDB IDs with chain mapping, resolution, experimental method (X-ray, cryo-EM, NMR), and UniProt sequence coverage. Essential for structural biologists to find the most suitable structure for a protein of interest. Example: P04637 (TP53) returns 641 structure entries, P00533 (EGFR) returns 633 entries, with X-ray and cryo-EM structures ranked by quality.

Parameters:

  • uniprot_accession (string) (required) UniProt accession for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1), ‘P01308’ (Insulin).

Example Usage:

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

PDBeSIFTS_get_pdb_to_uniprot (Type: PDBeSIFTSTool)

Map PDB entry chains to UniProt protein accessions using PDBe SIFTS cross-referencing. For a give…

PDBeSIFTS_get_pdb_to_uniprot tool specification

Tool Information:

  • Name: PDBeSIFTS_get_pdb_to_uniprot

  • Type: PDBeSIFTSTool

  • Description: Map PDB entry chains to UniProt protein accessions using PDBe SIFTS cross-referencing. For a given PDB structure, returns which UniProt proteins are present, which chains correspond to each protein, and the residue-level mapping between PDB and UniProt numbering. Essential for understanding multi-chain structures and identifying proteins in crystal/EM structures. Example: PDB 1tup maps chain A/B/C to P04637 (TP53) residues 94-312.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘1tup’ (p53-DNA complex), ‘1m17’ (EGFR kinase), ‘3pxe’ (BRCA1 BRCT), ‘4hhb’ (hemoglobin).

Example Usage:

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

PDBeSIFTS_get_scop_mapping (Type: PDBeSIFTSTool)

Get the SCOP (Structural Classification of Proteins) structural classification for a PDB entry fr…

PDBeSIFTS_get_scop_mapping tool specification

Tool Information:

  • Name: PDBeSIFTS_get_scop_mapping

  • Type: PDBeSIFTSTool

  • Description: Get the SCOP (Structural Classification of Proteins) structural classification for a PDB entry from PDBe SIFTS. Returns the SCOP hierarchy - class (e.g., ‘All beta proteins’), fold (e.g., ‘Lipocalins’), superfamily, SCCS code, and SCOP domain identifier - together with per-chain residue-range mappings showing which residues of each chain form each SCOP domain. SCOP classifies protein domains by evolutionary and structural relationships; this fold/superfamily information is otherwise absent from ToolUniverse. Use to determine the structural fold class of a crystal/EM structure and locate the domain boundaries per chain. Example: 1cbs -> SCOP sunid 50847, class ‘All beta proteins’, fold ‘Lipocalins’, superfamily ‘Lipocalins’, SCCS ‘b.60.1.2’, chain A residues 1-137.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘1cbs’ (cellular retinoic acid binding protein), ‘1tup’ (p53-DNA), ‘4hhb’ (hemoglobin), ‘1m17’ (EGFR kinase).

Example Usage:

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