PDB Entry Metadata: Title, Authors, Citation, Method and Resolution (RCSB PDB)

rcsbdata/pdb-entry

Returns the core metadata record of one Protein Data Bank (PDB) entry from its four-character PDB ID: structure title, deposition authors, primary citation with DOI and PubMed id, unit cell and space group, experimental method and resolution, deposition, release and revision dates, and entity, chain and atom counts. The response is large; use the GraphQL query tool to fetch only chosen 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/pdb-entry" })

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

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

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

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

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": [
    "entry_id"
  ],
  "properties": {
    "entry_id": {
      "type": "string",
      "pattern": "^[A-Za-z0-9]{4}$",
      "description": "The four-character PDB ID of the entry, for example 4HHB (human deoxyhaemoglobin)."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "required": [
    "rcsb_id",
    "entry",
    "struct"
  ],
  "properties": {
    "cell": {
      "type": "object",
      "description": "Unit cell lengths and angles."
    },
    "entry": {
      "type": "object",
      "description": "The entry block; `entry.id` is the PDB ID."
    },
    "exptl": {
      "type": "array",
      "items": {
        "type": "object"
      },
      "description": "Experimental method records."
    },
    "struct": {
      "type": "object",
      "description": "`struct.title` is the structure's title."
    },
    "rcsb_id": {
      "type": "string",
      "description": "The PDB ID, for example 4HHB."
    },
    "citation": {
      "type": "array",
      "items": {
        "type": "object"
      },
      "description": "Citations, including the primary one."
    },
    "symmetry": {
      "type": "object",
      "description": "Space group and international tables number."
    },
    "audit_author": {
      "type": "array",
      "items": {
        "type": "object"
      },
      "description": "The deposition authors."
    },
    "rcsb_entry_info": {
      "type": "object",
      "description": "Counts (entities, atoms, models), experimental method, molecular weight and resolution."
    },
    "struct_keywords": {
      "type": "object",
      "description": "Keyword fields such as `pdbx_keywords`."
    },
    "rcsb_accession_info": {
      "type": "object",
      "description": "Deposition, initial release and revision dates and status."
    },
    "rcsb_primary_citation": {
      "type": "object",
      "description": "The primary citation with journal, year, DOI and PubMed id."
    },
    "rcsb_entry_container_identifiers": {
      "type": "object",
      "description": "The entity, assembly and model ids of the entry."
    }
  },
  "description": "The core record of the PDB entry, as RCSB returns it.",
  "additionalProperties": true
}