pdb

name	pdb
description	RCSB PDB for 3D protein structures, resolution, and experimental methods

RCSB Protein Data Bank (PDB)

Overview

RCSB PDB hosts experimentally determined 3D structures of biological macromolecules solved by X-ray crystallography, cryo-EM, and NMR.

Search API

import requests

# Text search
url = "https://search.rcsb.org/rcsbsearch/v2/query"
query = {
    "query": {
        "type": "terminal",
        "service": "text",
        "parameters": {"attribute": "struct.title", "operator": "contains_words", "value": "kinase"}
    },
    "return_type": "entry"
}
r = requests.post(url, json=query)
pdb_ids = [hit["identifier"] for hit in r.json()["result_set"]]

Data API

# Fetch entry summary
r = requests.get("https://data.rcsb.org/rest/v1/core/entry/4HHB")
entry = r.json()

# Get polymer entities
r = requests.get("https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB/1")

GraphQL API

query_gql = '{ entry(entry_id: "4HHB") { struct { title } rcsb_entry_info { resolution_combined } } }'
r = requests.post("https://data.rcsb.org/graphql", json={"query": query_gql})

Key Details

• resolution_combined: In angstroms (lower is better; <2.0 is high-res).
• experimental_method: X-RAY DIFFRACTION, ELECTRON MICROSCOPY, SOLUTION NMR.
• PDB IDs are 4-character alphanumeric (e.g., 4HHB).
• Download: https://files.rcsb.org/download/{PDB_ID}.cif (or .pdb).
• Use Biopython PDBParser or MMCIFParser for local structure analysis.