RCSB PDB

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RCSB Protein Data Bank — experimental macromolecular structures. Keyless.

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Tools

rcsb_pdb_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), reso

No parameters required.

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polymer_entityrequired: pdb_id, entity_id

"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-referen

Parameters
NameTypeDescription
pdb_idreqstring—
entity_idreqstring—
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ligandrequired: pdb_id, ligand_id

"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

Parameters
NameTypeDescription
pdb_idreqstring—
ligand_idreqstring—
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assemblyrequired: pdb_id

"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

Parameters
NameTypeDescription
pdb_idreqstring—
assembly_idoptstring—
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rcsb_pdb_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

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/rcsb-pdb/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/rcsb-pdb/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"rcsb_pdb_search","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("rcsb_pdb_search", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("rcsb protein data bank — experimental macromolecular structures");