Pdb Database

RCSB Protein Data Bank

The Protein Data Bank hosts over 200,000 experimentally determined macromolecular structures plus computed models from AlphaFold and ModelArchive. This skill provides programmatic access to search, download, and analyze structural data.

Applicable Scenarios

Setup

pip install rcsb-api requests

The rcsb-api package (v1.5.0+) provides:

• rcsbapi.search - Query construction and execution
• rcsbapi.data - DataQuery for batch retrieval

Quick Reference

Search Queries

from rcsbapi.search import TextQuery, AttributeQuery, SeqSimilarityQuery, StructSimilarityQuery

# Text search
results = list(TextQuery("kinase inhibitor")())

# Filter by organism (use string attribute paths)
human = AttributeQuery(
    attribute="rcsb_entity_source_organism.scientific_name",
    operator="exact_match",
    value="Homo sapiens"
)

# Filter by resolution
high_res = AttributeQuery(
    attribute="rcsb_entry_info.resolution_combined",
    operator="less",
    value=2.0
)

# Filter by experimental method
xray = AttributeQuery(
    attribute="exptl.method",
    operator="exact_match",
    value="X-RAY DIFFRACTION"
)

# Combine queries: & (AND), | (OR), ~ (NOT)
results = list((TextQuery("kinase") & human & high_res)())

# Sequence similarity (MMseqs2) - minimum 25 residues required
seq_query = SeqSimilarityQuery(
    value="VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH",
    evalue_cutoff=1e-5,
    identity_cutoff=0.7
)

# Structure similarity (3D fold)
struct_query = StructSimilarityQuery(
    structure_search_type="entry_id",
    entry_id="4HHB"
)

Data Retrieval (REST API)

The rcsb-api package's data module has limited functionality. Use the REST API directly for metadata:

import requests

def fetch_entry(pdb_id: str) -> dict:
    """Fetch entry metadata from RCSB REST API."""
    resp = requests.get(f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}")
    resp.raise_for_status()
    return resp.json()

# Example usage
data = fetch_entry("4HHB")
print(data["struct"]["title"])
print(data["rcsb_entry_info"]["resolution_combined"])

# Polymer entity (chain info + sequence)
def fetch_polymer_entity(pdb_id: str, entity_id: int = 1) -> dict:
    resp = requests.get(f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}")
    resp.raise_for_status()
    return resp.json()

entity = fetch_polymer_entity("4HHB", 1)
sequence = entity["entity_poly"]["pdbx_seq_one_letter_code"]

File Downloads

import requests
from pathlib import Path

def download_structure(pdb_id: str, fmt: str = "cif", outdir: str = ".") -> Path:
    url = f"https://files.rcsb.org/download/{pdb_id}.{fmt}"
    resp = requests.get(url)
    resp.raise_for_status()
    outpath = Path(outdir) / f"{pdb_id}.{fmt}"
    outpath.write_text(resp.text)
    return outpath

Common Workflows

Find High-Quality Human Structures

from rcsbapi.search import TextQuery, AttributeQuery

query = (
    TextQuery("receptor") &
    AttributeQuery(
        attribute="rcsb_entity_source_organism.scientific_name",
        operator="exact_match",
        value="Homo sapiens"
    ) &
    AttributeQuery(
        attribute="rcsb_entry_info.resolution_combined",
        operator="less",
        value=2.5
    ) &
    AttributeQuery(
        attribute="exptl.method",
        operator="exact_match",
        value="X-RAY DIFFRACTION"
    )
)
results = list(query())

Batch Metadata Retrieval

import requests
import time

def fetch_batch(pdb_ids: list, delay: float = 0.3) -> dict:
    """Fetch metadata with rate limiting."""
    results = {}
    for pdb_id in pdb_ids:
        try:
            resp = requests.get(f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}")
            resp.raise_for_status()
            data = resp.json()
            results[pdb_id] = {
                "title": data["struct"]["title"],
                "resolution": data.get("rcsb_entry_info", {}).get("resolution_combined"),
                "method": data.get("exptl", [{}])[0].get("method"),
            }
        except Exception as e:
            results[pdb_id] = {"error": str(e)}
        time.sleep(delay)
    return results

Find Drug-Bound Structures

from rcsbapi.search import AttributeQuery

# Find structures containing imatinib (ligand ID: STI)
query = AttributeQuery(
    attribute="rcsb_nonpolymer_entity_instance_container_identifiers.comp_id",
    operator="exact_match",
    value="STI"
)
drug_complexes = list(query())

GraphQL for Complex Queries

import requests

query = """
{
  entry(entry_id: "4HHB") {
    struct { title }
    rcsb_entry_info {
      resolution_combined
      deposited_atom_count
    }
    polymer_entities {
      rcsb_polymer_entity { pdbx_description }
      entity_poly { pdbx_seq_one_letter_code }
    }
  }
}
"""

response = requests.post(
    "https://data.rcsb.org/graphql",
    json={"query": query}
)
result = response.json()["data"]["entry"]

Key Concepts

Common Attribute Paths

Use these string paths with AttributeQuery:

Best Practices

Troubleshooting

References

See references/api-reference.md for:

• Complete REST endpoint documentation
• All searchable attributes and operators
• Advanced query patterns
• Rate limiting strategies

External Links

• RCSB PDB: https://www.rcsb.org
• API Overview: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
• Python Package: https://rcsbapi.readthedocs.io/
• GraphQL Explorer: https://data.rcsb.org/graphql