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 OpenAI Agents SDK 2 tools — connect in under 2 minutes

Name: RCSB PDB
Availability: InStock
Author: Vinkius

openai.github.io/openai-agents-python/mcp

Built by Vinkius GDPR 2 Tools SDK

The OpenAI Agents SDK enables production-grade agent workflows in Python. Connect RCSB PDB through Vinkius and your agents gain typed, auto-discovered tools with built-in guardrails. no manual schema definitions required.

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 agents import Agent, Runner
from agents.mcp import MCPServerStreamableHttp

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

        agent = Agent(
            name="RCSB PDB Assistant",
            instructions=(
                "You help users interact with RCSB PDB. "
                "You have access to 2 tools."
            ),
            mcp_servers=[mcp_server],
        )

        result = await Runner.run(
            agent, "List all available tools from RCSB PDB"
        )
        print(result.final_output)

asyncio.run(main())

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* 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.

The OpenAI Agents SDK auto-discovers all 2 tools from RCSB PDB through native MCP integration. Build agents with built-in guardrails, tracing, and handoff patterns. chain multiple agents where one queries RCSB PDB, another analyzes results, and a third generates reports, all orchestrated through Vinkius.

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 OpenAI Agents SDK 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 OpenAI Agents SDK via MCP

Follow these steps to integrate the RCSB PDB MCP Server with OpenAI Agents SDK.

Install the SDK

Run pip install openai-agents in your Python environment

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.com

Run the script

Save the code above and run it: python agent.py

Explore tools

The agent will automatically discover 2 tools from RCSB PDB

Why Use OpenAI Agents SDK with the RCSB PDB MCP Server

OpenAI Agents SDK provides unique advantages when paired with RCSB PDB through the Model Context Protocol.

Native MCP integration via `MCPServerSse`, pass the URL and the SDK auto-discovers all tools with full type safety

Built-in guardrails, tracing, and handoff patterns let you build production-grade agents without reinventing safety infrastructure

Lightweight and composable: chain multiple agents and MCP servers in a single pipeline with minimal boilerplate

First-party OpenAI support ensures optimal compatibility with GPT models for tool calling and structured output

RCSB PDB + OpenAI Agents SDK Use Cases

Practical scenarios where OpenAI Agents SDK combined with the RCSB PDB MCP Server delivers measurable value.

Automated workflows: build agents that query RCSB PDB, process the data, and trigger follow-up actions autonomously

Multi-agent orchestration: create specialist agents. one queries RCSB PDB, another analyzes results, a third generates reports

Data enrichment pipelines: stream data through RCSB PDB tools and transform it with OpenAI models in a single async loop

Customer support bots: agents query RCSB PDB to resolve tickets, look up records, and update statuses without human intervention

RCSB PDB MCP Tools for OpenAI Agents SDK (2)

These 2 tools become available when you connect RCSB PDB to OpenAI Agents SDK 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 OpenAI Agents SDK

Ready-to-use prompts you can give your OpenAI Agents SDK 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 OpenAI Agents SDK

Common issues when connecting RCSB PDB to OpenAI Agents SDK through the Vinkius, and how to resolve them.

MCPServerStreamableHttp not found

Ensure you have the latest version: pip install --upgrade openai-agents

Agent not calling tools

Make sure your prompt explicitly references the task the tools can help with.

RCSB PDB + OpenAI Agents SDK FAQ

Common questions about integrating RCSB PDB MCP Server with OpenAI Agents SDK.

How does the OpenAI Agents SDK connect to MCP?

Use MCPServerSse(url=...) to create a server connection. The SDK auto-discovers all tools and makes them available to your agent with full type information.