# PDB Structure Lookup (`researchdata/pdb-structure-lookup`) Actor

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

- **URL**: https://apify.com/researchdata/pdb-structure-lookup.md
- **Developed by:** [Research Analyst](https://apify.com/researchdata) (community)
- **Security:** Limited permissions
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $1.40 / 1,000 structure returneds

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

An Actor is a serverless cloud program that runs on the Apify platform. It has two run modes.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.

Apify vocabulary and the platform model are defined once, in the agent quickstart at https://apify.com/agents.md.

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.

Do not guess an integration path. Every one of them is in the agent quickstart at https://apify.com/agents.md: the Apify MCP server, Agent Skills with the Apify CLI, the JavaScript and Python clients, the REST API, and the account-free path for an agent with no human to sign in. It also carries the rule on stating cost before the first paid run.

For examples already wired to this Actor's own input schema, see the [API](#api) section below.

Each client library has reference documentation the quickstart does not restate: [JavaScript/TypeScript](https://docs.apify.com/api/client/js/docs.md) (`npm install apify-client`) and [Python](https://docs.apify.com/api/client/python/docs.md) (`pip install apify-client`).

# README

## 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:

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

### Output (one dataset item per result)

```json
{
  "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.

# Actor input Schema

## `pdbIds` (type: `array`):

List of 4-character PDB IDs, e.g. 4HHB, 7F1T.

## `query` (type: `string`):

Optional full-text search (e.g. 'GPR84', 'adhesion GPCR cryo-EM').

## `maxResults` (type: `integer`):

Cap for search hits.

## Actor input object example

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

# Actor output Schema

## `results` (type: `string`):

No description

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "pdbIds": [
        "4HHB",
        "6VXX"
    ]
};

// Run the Actor and wait for it to finish
const run = await client.actor("researchdata/pdb-structure-lookup").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = { "pdbIds": [
        "4HHB",
        "6VXX",
    ] }

# Run the Actor and wait for it to finish
run = client.actor("researchdata/pdb-structure-lookup").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "pdbIds": [
    "4HHB",
    "6VXX"
  ]
}' |
apify call researchdata/pdb-structure-lookup --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,researchdata/pdb-structure-lookup"
        }
    }
}
```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/9VxZ9YjRuUdoLWgT1/builds/Yp66nkYGYR1e5uFbR/openapi.json