RCSB PDB Python API Docs | dltHub

RCSB PDB provides REST APIs for accessing protein structure data, including the Data API for static data and the Search API for querying entries. The RCSB PDB Data API uses JSON Schema for data schemas. The File Download Services offer access to various protein structure files in different formats. The REST API base URL is https://data.rcsb.org/rest/v1 and No authentication required for public GET endpoints.

dlt is an open-source Python library that handles authentication, pagination, and schema evolution automatically. dlthub provides AI context files that enable code assistants to generate production-ready pipelines. Install with uv pip install "dlt[workspace]" and start loading RCSB PDB data in under 10 minutes.

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What data can I load from RCSB PDB?

Here are some of the endpoints you can load from RCSB PDB:

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How do I authenticate with the RCSB PDB API?

RCSB PDB Data and Search REST APIs are public; no API key or bearer token is required for standard GET requests. Use standard HTTP(S) headers (e.g., Accept: application/json) where needed.

1. Get your credentials

No credentials required; the RCSB PDB REST API is public and can be accessed without authentication.

2. Add them to .dlt/secrets.toml

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[sources.rcsb_pdb_source]

dlt reads this automatically at runtime — never hardcode tokens in your pipeline script. For production environments, see setting up credentials with dlt for environment variable and vault-based options.

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How do I set up and run the pipeline?

Set up a virtual environment and install dlt:

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uv venv && source .venv/bin/activate
uv pip install "dlt[workspace]"

1. Install the dlt AI Workbench:

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dlt ai init --agent <your-agent> # <agent>: claude | cursor | codex

This installs project rules, a secrets management skill, appropriate ignore files, and configures the dlt MCP server for your agent. Learn more →

2. Install the rest-api-pipeline toolkit:

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dlt ai toolkit rest-api-pipeline install

This loads the skills and context about dlt the agent uses to build the pipeline iteratively, efficiently, and safely. The agent uses MCP tools to inspect credentials — it never needs to read your secrets.toml directly. Learn more →

3. Start LLM-assisted coding:

Use /find-source to load data from the RCSB PDB API into DuckDB.

The rest-api-pipeline toolkit takes over from here — it reads relevant API documentation, presents you with options for which endpoints to load, and follows a structured workflow to scaffold, debug, and validate the pipeline step by step.

4. Run the pipeline:

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python rcsb_pdb_pipeline.py

If everything is configured correctly, you'll see output like this:

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Pipeline rcsb_pdb_pipeline load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset rcsb_pdb_data
The duckdb destination used duckdb:/rcsb_pdb.duckdb location to store data
Load package 1749667187.541553 is LOADED and contains no failed jobs

Inspect your pipeline and data:

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dlt pipeline rcsb_pdb_pipeline show

This opens the Pipeline Dashboard where you can verify pipeline state, load metrics, schema (tables, columns, types), and query the loaded data directly.

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Python pipeline example

This example loads entry and search_query from the RCSB PDB API into DuckDB. It mirrors the endpoint and data selector configuration from the table above:

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import dlt
from dlt.sources.rest_api import RESTAPIConfig, rest_api_resources

@dlt.source
def rcsb_pdb_source(=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://data.rcsb.org/rest/v1",
            "auth": {
                "type": "none",
                "": ,
            },
        },
        "resources": [
            {"name": "entry", "endpoint": {"path": "core/entry/{entry_id}"}},
            {"name": "search_query", "endpoint": {"path": "rcsbsearch/v2/query", "data_selector": "result_set"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="rcsb_pdb_pipeline",
        destination="duckdb",
        dataset_name="rcsb_pdb_data",
    )
    load_info = pipeline.run(rcsb_pdb_source())
    print(load_info)

To add more endpoints, append entries from the resource table to the "resources" list using the same name, path, and data_selector pattern.

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How do I query the loaded data?

Once the pipeline runs, dlt creates one table per resource. You can query with Python or SQL.

Python (pandas DataFrame):

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import dlt

data = dlt.pipeline("rcsb_pdb_pipeline").dataset()
sessions_df = data.entry.df()
print(sessions_df.head())

SQL (DuckDB example):

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SELECT * FROM rcsb_pdb_data.entry LIMIT 10;

In a marimo or Jupyter notebook:

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import dlt

data = dlt.pipeline("rcsb_pdb_pipeline").dataset()
data.entry.df().head()

See how to explore your data in marimo Notebooks and how to query your data in Python with dataset.

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What destinations can I load RCSB PDB data to?

dlt supports loading into any of these destinations — only the destination parameter changes:

Change the destination in dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. See the full destinations list.

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Next steps

Continue your data engineering journey with the other toolkits of the dltHub AI Workbench:

• data-exploration — Build custom notebooks, charts, and dashboards for deeper analysis with marimo notebooks.
• dlthub-runtime — Deploy, schedule, and monitor your pipeline in production.

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dlt ai toolkit data-exploration install
dlt ai toolkit dlthub-runtime install

• How to deploy a pipeline
• How to explore your data in marimo Notebooks
• How to query your data in Python with dataset
• Join the dlt community on Slack