PDB GraphQL Query: Choose Your Own Fields from the Protein Data Bank (RCSB PDB)

rcsbdata/graphql-query

Runs a GraphQL query against the RCSB Protein Data Bank Data API and returns just the fields you ask for, for example the title of a PDB entry with `{entry(entry_id:"4HHB"){struct{title}}}`. Use it instead of the full entry record when you want a small answer, or to reach entities, assemblies and other levels of the structure in one request. A query the server rejects is returned as an error. The answer is as large as the fields you select: a query that selects many entries or deeply nested fields (sequences, features) can return megabytes, so ask for fewer ids or fewer fields. PDB data is CC0, but fields that come from integrated outside resources can carry those resources' own licences. Served by Eden Engine; not an official RCSB PDB product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.

Data source

RCSB Protein Data Bank

Data from the RCSB Protein Data Bank (RCSB PDB, rcsb.org); PDB archive data is released under CC0 1.0, and data from integrated external resources carries that resource's own licence. Users are encouraged to credit the original authors of a PDB structure. Served by Eden Engine; not an official RCSB PDB product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "rcsbdata/graphql-query" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "rcsbdata/graphql-query" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "rcsbdata/graphql-query", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "rcsbdata/graphql-query", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

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Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "query"
  ],
  "properties": {
    "query": {
      "type": "string",
      "maxLength": 4000,
      "minLength": 2,
      "description": "The GraphQL query text, for example {entry(entry_id:\"4HHB\"){struct{title}}}. Do not URL-encode it."
    },
    "variables": {
      "type": "string",
      "maxLength": 2000,
      "description": "Optional. A JSON object, as a string, giving values for the variables the query declares, for example {\"id\":\"4HHB\"}."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "description": "The `data` object of the GraphQL response: one key per root field in the query, holding exactly the fields requested.",
  "additionalProperties": true
}