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.