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

Task	Examples
Structure Retrieval	Download coordinates for a known PDB ID
Similarity Search	Find structures similar by sequence or 3D fold
Metadata Access	Get resolution, method, organism, ligands
Dataset Building	Compile structures for ML training or analysis
Drug Discovery	Identify ligand-bound structures for a target
Quality Filtering	Select high-resolution, well-refined structures

Setup

bash

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

python

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:

python

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

Format	URL Pattern
PDB	`https://files.rcsb.org/download/{ID}.pdb`
mmCIF	`https://files.rcsb.org/download/{ID}.cif`
Assembly	`https://files.rcsb.org/download/{ID}.pdb1`
FASTA	`https://www.rcsb.org/fasta/entry/{ID}`

python

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

python

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

python

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

python

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

python

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

Term	Definition
PDB ID	4-character alphanumeric code (e.g., "4HHB"). AlphaFold uses "AF_" prefix
Entity	Distinct molecular species. A homodimer has one entity appearing twice
Resolution	Quality metric in angstroms. Lower is better; <2.0 Å is high quality
Biological Assembly	Functional oligomeric state (may differ from asymmetric unit)
mmCIF	Modern format replacing legacy PDB; required for large structures

Common Attribute Paths

Use these string paths with

AttributeQuery

Attribute	Description
`rcsb_entity_source_organism.scientific_name`	Source organism (e.g., "Homo sapiens")
`rcsb_entry_info.resolution_combined`	Resolution in angstroms
`exptl.method`	Experimental method (X-RAY DIFFRACTION, ELECTRON MICROSCOPY, SOLUTION NMR)
`rcsb_nonpolymer_entity_instance_container_identifiers.comp_id`	Ligand/small molecule ID
`struct.title`	Structure title
`rcsb_accession_info.deposit_date`	Deposition date

Best Practices

Practice	Rationale
Use mmCIF format	PDB format has atom count limits
Filter by resolution	<2.5 Å for most analyses; <2.0 Å for detailed work
Check experimental method	X-ray vs cryo-EM vs NMR have different quality metrics
Rate limit requests	2-3 req/s to avoid 429 errors
Cache downloads	Structures rarely change after release
Prefer GraphQL	Reduces requests for complex data needs

Troubleshooting

Issue	Resolution
404 on entry fetch	Entry may be obsoleted; check RCSB website for superseding ID
429 Too Many Requests	Implement exponential backoff; reduce request rate
Empty search results	Check query syntax; use `query.to_dict()` to debug
Large structure fails	Use mmCIF format instead of PDB
Missing sequence data	Query polymer entity endpoint, not entry

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

pdb-database

NPX Install

Tags

SKILL.md Content

RCSB Protein Data Bank

Applicable Scenarios

Setup

Quick Reference

Search Queries

Data Retrieval (REST API)

File Downloads

Common Workflows

Find High-Quality Human Structures

Batch Metadata Retrieval

Find Drug-Bound Structures

GraphQL for Complex Queries

Key Concepts

Common Attribute Paths

Best Practices

Troubleshooting

References

External Links