pdb-structure-api

RCSB Protein Data Bank API Guide

Overview

The RCSB Protein Data Bank (PDB) is the single global archive for experimentally determined 3D structures of biological macromolecules. It hosts over 200,000 structures resolved by X-ray crystallography, cryo-EM, NMR spectroscopy, and other methods. Each entry includes atomic coordinates, experimental metadata, polymer sequences, bound ligands, and literature references.

Two complementary APIs are available. The Data API (data.rcsb.org) serves structured entry metadata, polymer entities, and chemical components via RESTful GET endpoints. The Search API (search.rcsb.org) supports full-text, attribute-based, sequence similarity, and structure similarity searches.

Authentication

No authentication required. Both APIs are freely accessible without API keys, tokens, or registration.

Core Endpoints

Data API: Get Entry by PDB ID

Retrieve metadata for a structure including experimental method, resolution, citations, and bound components.

• URL: GET https://data.rcsb.org/rest/v1/core/entry/{pdb_id}

curl "https://data.rcsb.org/rest/v1/core/entry/4HHB"

• Response (key fields):

{
  "rcsb_id": "4HHB",
  "struct": {
    "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION"
  },
  "exptl": [{"method": "X-RAY DIFFRACTION"}],
  "rcsb_entry_info": {
    "deposited_atom_count": 4779,
    "molecular_weight": 64.74,
    "polymer_composition": "heteromeric protein",
    "polymer_entity_count_protein": 2,
    "resolution_combined": [1.74],
    "nonpolymer_bound_components": ["HEM"]
  }
}

Data API: Get Polymer Entity

Retrieve protein/nucleic acid entity details including sequence, organism, and gene info.

• URL: GET https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}

curl "https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB/1"

• Response (key fields):

{
  "entity_poly": {
    "pdbx_seq_one_letter_code_can": "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH...",
    "rcsb_entity_polymer_type": "Protein",
    "rcsb_sample_sequence_length": 141,
    "type": "polypeptide(L)"
  },
  "entity_src_gen": [{
    "gene_src_common_name": "Human",
    "pdbx_gene_src_scientific_name": "Homo sapiens",
    "pdbx_gene_src_ncbi_taxonomy_id": "9606"
  }]
}