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 Mastra AI 2 tools — connect in under 2 minutes

Name: RCSB PDB
Availability: InStock
Author: Vinkius

docs.mastra.ai/docs/agents/mcp-tools

Built by Vinkius GDPR 2 Tools SDK

Mastra AI is a TypeScript-native agent framework built for modern web stacks. Connect RCSB PDB through Vinkius and Mastra agents discover all tools automatically. type-safe, streaming-ready, and deployable anywhere Node.js runs.

Get MCP Server for AI Agents

ASK AI ABOUT THIS MCP SERVER

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typescript

import { Agent } from "@mastra/core/agent";
import { createMCPClient } from "@mastra/mcp";
import { openai } from "@ai-sdk/openai";

async function main() {
  // Your Vinkius token. get it at cloud.vinkius.com
  const mcpClient = await createMCPClient({
    servers: {
      "rcsb-pdb": {
        url: "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
      },
    },
  });

  const tools = await mcpClient.getTools();
  const agent = new Agent({
    name: "RCSB PDB Agent",
    instructions:
      "You help users interact with RCSB PDB " +
      "using 2 tools.",
    model: openai("gpt-4o"),
    tools,
  });

  const result = await agent.generate(
    "What can I do with RCSB PDB?"
  );
  console.log(result.text);
}

main();

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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.

Mastra's agent abstraction provides a clean separation between LLM logic and RCSB PDB tool infrastructure. Connect 2 tools through Vinkius and use Mastra's built-in workflow engine to chain tool calls with conditional logic, retries, and parallel execution. deployable to any Node.js host in one command.

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 Mastra 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 Mastra AI via MCP

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

Install dependencies

Run npm install @mastra/core @mastra/mcp @ai-sdk/openai

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Run the agent

Save to agent.ts and run with npx tsx agent.ts

Explore tools

Mastra discovers 2 tools from RCSB PDB via MCP

Why Use Mastra AI with the RCSB PDB MCP Server

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

Mastra's agent abstraction provides a clean separation between LLM logic and tool infrastructure. add RCSB PDB without touching business code

Built-in workflow engine chains MCP tool calls with conditional logic, retries, and parallel execution for complex automation

TypeScript-native: full type inference for every RCSB PDB tool response with IDE autocomplete and compile-time checks

One-command deployment to any Node.js host. Vercel, Railway, Fly.io, or your own infrastructure

RCSB PDB + Mastra AI Use Cases

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

Automated workflows: build multi-step agents that query RCSB PDB, process results, and trigger downstream actions in a typed pipeline

SaaS integrations: embed RCSB PDB as a first-class tool in your product's AI features with Mastra's clean agent API

Background jobs: schedule Mastra agents to query RCSB PDB on a cron and store results in your database automatically

Multi-agent systems: create specialist agents that collaborate using RCSB PDB tools alongside other MCP servers

RCSB PDB MCP Tools for Mastra AI (2)

These 2 tools become available when you connect RCSB PDB to Mastra 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