`get_molecules`

Pack: pdbe · Endpoint: https://gateway.pipeworx.io/pdbe/mcp

PDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like “1cbs”.

Parameters

Name	Type	Required	Description
`pdb_id`	string	yes	A 4-char PDB id, e.g. “1cbs”.

Example call

Arguments

{
  "pdb_id": "1cbs"
}

curl

curl -X POST https://gateway.pipeworx.io/pdbe/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"get_molecules","arguments":{"pdb_id":"1cbs"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('get_molecules', {
  "pdb_id": "1cbs"
});

More examples

{
  "pdb_id": "4hhb"
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "pdbe": {
      "url": "https://gateway.pipeworx.io/pdbe/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

get_molecules