What experimental methods are represented in the PDB?

The PDB contains structures determined by four main methods: X-ray Crystallography (85% of entries, atomic resolution), Cryo-EM (rapidly growing, now 15%+ of new deposits), NMR Spectroscopy (solution-state structures), and Neutron Diffraction (hydrogen atom positions). Each entry lists its method and resolution.

Do I need authentication to access PDB data?

No. RCSB PDB is completely free and open — funded by NSF, NIH, DOE, and international partners. All 220K+ structures are openly accessible without any registration or API key. The data is licensed under CC0 (public domain).

What information does each PDB entry contain?

Each entry includes: PDB ID (4-character code), structure title, depositing authors, experimental method, resolution in Ångströms, source organism, release date, number of polymer chains, and bound non-polymer ligands (drugs, cofactors, ions). Higher resolution (lower number) means more precise atomic coordinates.

RCSB PDB MCP Server for Pydantic AI 2 tools — connect in under 2 minutes

Name: RCSB PDB
Availability: InStock
Author: Vinkius

ai.pydantic.dev/mcp

Built by Vinkius GDPR 2 Tools SDK

Pydantic AI brings type-safe agent development to Python with first-class MCP support. Connect RCSB PDB through Vinkius and every tool is automatically validated against Pydantic schemas. catch errors at build time, not in production.

Get MCP Server for AI Agents

ASK AI ABOUT THIS MCP SERVER

Open in ChatGPT Open in Claude Open in Perplexity

Vinkius supports streamable HTTP and SSE.

python

import asyncio
from pydantic_ai import Agent
from pydantic_ai.mcp import MCPServerHTTP

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    server = MCPServerHTTP(url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")

    agent = Agent(
        model="openai:gpt-4o",
        mcp_servers=[server],
        system_prompt=(
            "You are an assistant with access to RCSB PDB "
            "(2 tools)."
        ),
    )

    result = await agent.run(
        "What tools are available in RCSB PDB?"
    )
    print(result.data)

asyncio.run(main())

Fully ManagedVinkius Servers

60%Token savings

High SecurityEnterprise-grade

IAMAccess control

EU AI ActCompliant

DLPData protection

V8 IsolateSandboxed

Ed25519Audit chain

<40msKill switch

Stream every event to Splunk, Datadog, or your own webhook in real-time

* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure

About RCSB PDB MCP Server

Connect your AI agent to the RCSB Protein Data Bank — the world's repository of experimentally determined 3D structural data for biological macromolecules.

Pydantic AI validates every RCSB PDB tool response against typed schemas, catching data inconsistencies at build time. Connect 2 tools through Vinkius and switch between OpenAI, Anthropic, or Gemini without changing your integration code. full type safety, structured output guarantees, and dependency injection for testable agents.

What you can do

Structure Search — Find protein, DNA, and RNA structures by name, function, disease association, or organism across 220K+ experimentally determined entries
PDB Entry Lookup — Get complete structural details by 4-character PDB ID (e.g., 1HHO for hemoglobin, 6LU7 for SARS-CoV-2 main protease) including experimental method, resolution, and bound molecules

The RCSB PDB MCP Server exposes 2 tools through the Vinkius. Connect it to Pydantic AI in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect RCSB PDB to Pydantic AI via MCP

Follow these steps to integrate the RCSB PDB MCP Server with Pydantic AI.

Install Pydantic AI

Run pip install pydantic-ai

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Run the agent

Save to agent.py and run: python agent.py

Explore tools

The agent discovers 2 tools from RCSB PDB with type-safe schemas

Why Use Pydantic AI with the RCSB PDB MCP Server

Pydantic AI provides unique advantages when paired with RCSB PDB through the Model Context Protocol.

Full type safety: every MCP tool response is validated against Pydantic models, catching data inconsistencies before they reach your application

Model-agnostic architecture. switch between OpenAI, Anthropic, or Gemini without changing your RCSB PDB integration code

Structured output guarantee: Pydantic AI ensures tool results conform to defined schemas, eliminating runtime type errors

Dependency injection system cleanly separates your RCSB PDB connection logic from agent behavior for testable, maintainable code

RCSB PDB + Pydantic AI Use Cases

Practical scenarios where Pydantic AI combined with the RCSB PDB MCP Server delivers measurable value.

Type-safe data pipelines: query RCSB PDB with guaranteed response schemas, feeding validated data into downstream processing

API orchestration: chain multiple RCSB PDB tool calls with Pydantic validation at each step to ensure data integrity end-to-end

Production monitoring: build validated alert agents that query RCSB PDB and output structured, schema-compliant notifications

Testing and QA: use Pydantic AI's dependency injection to mock RCSB PDB responses and write comprehensive agent tests

RCSB PDB MCP Tools for Pydantic AI (2)

These 2 tools become available when you connect RCSB PDB to Pydantic AI via MCP:

get_pdb_structure

PDB IDs are 4-character codes like 1HHO, 6LU7, 7BNN. Get full structural details by PDB ID

search_pdb

Returns PDB ID, title, experimental method (X-ray, Cryo-EM, NMR), resolution, authors, and bound ligands. Essential for drug discovery and structural biology. Search 220K+ 3D molecular structures in the Protein Data Bank

Example Prompts for RCSB PDB in Pydantic AI

Ready-to-use prompts you can give your Pydantic AI agent to start working with RCSB PDB immediately.

"Show me the structure of the SARS-CoV-2 main protease."

"Get full structural details for PDB entry 1HHO — what protein is it?"

"Find all cryo-EM structures of ribosome complexes."

Troubleshooting RCSB PDB MCP Server with Pydantic AI

Common issues when connecting RCSB PDB to Pydantic AI through the Vinkius, and how to resolve them.

MCPServerHTTP not found

Update: pip install --upgrade pydantic-ai

RCSB PDB + Pydantic AI FAQ

Common questions about integrating RCSB PDB MCP Server with Pydantic AI.

How does Pydantic AI discover MCP tools?

Create an MCPServerHTTP instance with the server URL. Pydantic AI connects, discovers all tools, and generates typed Python interfaces automatically.

Does Pydantic AI validate MCP tool responses?

Yes. When you define result types as Pydantic models, every tool response is validated against the schema. Invalid data raises a clear error instead of silently corrupting your pipeline.

Can I switch LLM providers without changing MCP code?

Absolutely. Pydantic AI abstracts the model layer. your RCSB PDB MCP integration works identically with OpenAI, Anthropic, Google, or any supported provider.