rcsb-pdb 6 tools

MCP server exposing 6 tools for rcsb-pdb.

Endpoint

This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.

POST https://gateway.pipeworx.io/rcsb-pdb/mcp
Content-Type: application/json

{"jsonrpc":"2.0","id":1,"method":"tools/list"}

Tools

• search — "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 PDB IDs you can pass to `structure` or `summary`. Use for structural biology, drug design, protein characterization.
• structure — "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 a specific structure.
• polymer_entity — "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.
• ligand — "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.
• assembly — "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 than the crystal contents.
• summary — 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`.

Full documentation

Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/rcsb-pdb/

About Pipeworx

Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io