MCP server

Rcsb Pdb

io.github.pipeworx-io/rcsb-pdb

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

RCSB PDB MCP — experimentally determined macromolecular structures.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

48

Token cost

About 27,267 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http rcsb-pdb https://gateway.pipeworx.io/rcsb-pdb/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.rcsb-pdb]
url = "https://gateway.pipeworx.io/rcsb-pdb/mcp"

Gemini CLI

{"mcpServers":{"rcsb-pdb":{"httpUrl":"https://gateway.pipeworx.io/rcsb-pdb/mcp"}}}

Cursor

{"mcpServers":{"rcsb-pdb":{"url":"https://gateway.pipeworx.io/rcsb-pdb/mcp"}}}

VS Code

{"servers":{"rcsb-pdb":{"type":"http","url":"https://gateway.pipeworx.io/rcsb-pdb/mcp"}}}

Antigravity

agy mcp add rcsb-pdb https://gateway.pipeworx.io/rcsb-pdb/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"rcsb-pdb","server_url":"https://gateway.pipeworx.io/rcsb-pdb/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"rcsb-pdb","server_url":"https://gateway.pipeworx.io/rcsb-pdb/mcp"}

Tools

• assembly ~161 tokens
  "Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather t
• ligand ~141 tokens
  "Ligand / cofactor / drug bound to [pdb_id]" / "small molecule in [PDB entry]" — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD.
• polymer_entity ~146 tokens
  "Chain [N] of PDB [ID]" / "sequence of chain in [pdb_id]" — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-references, GO annotations. Use to drill into one chain of a multi-chain structure.
• search ~256 tokens
  "Find protein structure of [target]" / "search PDB for [protein]" / "is there a crystal structure of [X]" / "[disease target] structures" / "CRISPR / kinase / GPCR structures" — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching
• structure ~142 tokens
  "PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]" — full PDB entry record by ID (e.g. "1abc", "7BV2"). Returns experimental method (X-ray / cryo-EM / NMR), resolution, authors, deposition date, organism, ligands, related entities. Use after `search` to inspect
• summary ~118 tokens
  Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of `structure`.

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