PDB Structure Lookup

Get clean metadata for Protein Data Bank structures by PDB ID or keyword: method, resolution, ligands, release date, primary citation and DOI.

Why use it

• Build structure tables for reviews, theses and grant proposals
• Feed AI agents with verified structural metadata instead of hallucinated values
• Track how many structures exist for a target family and at what resolution

No API keys, no scraping of HTML – the actor talks to the official public API, handles paging, rate limits and retries, and returns flat JSON you can export as CSV/Excel or call from code, Make, Zapier, n8n or AI agents (Apify MCP server).

Input

Field	Title	Description
pdbIds	PDB IDs	List of 4-character PDB IDs, e.g. 4HHB, 7F1T.
query	Search query	Optional full-text search (e.g. 'GPR84', 'adhesion GPCR cryo-EM').
maxResults	Max results from search	Cap for search hits.

Example input:

{
  "pdbIds": [
    "4HHB",
    "6VXX"
  ],
  "maxResults": 25
}

Output (one dataset item per result)

{
  "pdbId": "4HHB",
  "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION",
  "methods": [
    "X-RAY DIFFRACTION"
  ],
  "resolutionA": 1.74,
  "ligands": [
    "HEM",
    "PO4"
  ],
  "releaseDate": "1984-07-17T00:00:00+0000",
  "doi": "10.1016/0022-2836(84)90472-8",
  "url": "https://www.rcsb.org/structure/4HHB"
}

Use with AI agents (Apify MCP server)

Add the Apify MCP server (https://mcp.apify.com) to Claude, Cursor or any MCP client and enable this actor (researchdata/pdb-structure-lookup). The agent can then call it directly: describe what you need, the agent fills the input fields above, runs the actor and reads the dataset. Because results are flat JSON with explicit nulls, an agent can use them without extra parsing. Set a maximum cost per run to keep agent calls capped.

Pricing

Pay per event: $0.002 per result (structure returned). You only pay for results you get; set a max cost per run to cap spending. Higher Apify plans get automatic volume discounts: Bronze −10 %, Silver −20 %, Gold −30 %.

Cost example

At $0.002 per result: 50 results ≈ $0.10, 1,000 results ≈ $2.00. Set a maximum cost per run in the run options to cap spending.

Limits

• Data comes from the provider's public API; fields the provider does not publish are returned empty (null), never guessed.
• Results reflect the provider's database at run time.
• Not affiliated with the data provider.
• Metadata and links only: the actor does not download coordinate files.

FAQ

Does it download coordinates?
No, metadata and links only.

What is the data license?
RCSB PDB data are CC0.

Data source & terms

RCSB PDB Data & Search APIs (public, CC0 data). Please respect the data provider's terms and cite the original resource in publications. This actor is an independent tool and is not affiliated with or endorsed by the data provider.