---
name: query-pdb-8b6b83a628fa
description: Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".
---

# RCSB PDB Database Query

Query the RCSB Protein Data Bank for experimental 3D structures.

## When to Use

- User asks for experimental structures of a protein
- User provides a PDB ID (e.g., "6LU7")
- User wants to find structures solved by X-ray, cryo-EM, or NMR
- User asks about resolution, ligands, or binding sites

## How to Execute

```python
import requests
import json

# 1. Text search (simple keyword)
def search_pdb(query_text, max_results=5):
    url = "https://search.rcsb.org/rcsbsearch/v2/query"
    query = {
        "query": {
            "type": "terminal",
            "service": "full_text",
            "parameters": {"value": query_text}
        },
        "return_type": "entry",
        "request_options": {"paginate": {"start": 0, "rows": max_results}}
    }
    r = requests.post(url, json=query)
    r.raise_for_status()
    return r.json()

# 2. Advanced search (by gene + organism + method)
def advanced_search_pdb(gene_name, organism="Homo sapiens", method=None, max_results=5):
    nodes = [
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.rcsb_gene_name.value",
                        "operator": "exact_match", "value": gene_name}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.ncbi_scientific_name",
                        "operator": "exact_match", "value": organism}}
    ]
    if method:
        nodes.append({"type": "terminal", "service": "text",
                      "parameters": {"attribute": "exptl.method", "operator": "exact_match", "value": method}})
    query = {
        "query": {"type": "group", "logical_operator": "and", "nodes": nodes},
        "return_type": "entry",
        "request_options": {"paginate": {"start": 0, "rows": max_results},
                           "sort": [{"sort_by": "rcsb_accession_info.deposit_date", "direction": "desc"}]}
    }
    r = requests.post("https://search.rcsb.org/rcsbsearch/v2/query", json=query)
    r.raise_for_status()
    return r.json()

# 3. Get entry details
def get_pdb_entry(pdb_id):
    url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
    r = requests.get(url)
    r.raise_for_status()
    return r.json()

# 4. Download structure
def download_pdb(pdb_id, output_dir="/workspace/group"):
    url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
    r = requests.get(url)
    r.raise_for_status()
    path = f"{output_dir}/{pdb_id}.pdb"
    with open(path, 'w') as f:
        f.write(r.text)
    return path

# Example
results = search_pdb("human insulin")
for hit in results.get("result_set", []):
    pdb_id = hit["identifier"]
    details = get_pdb_entry(pdb_id)
    title = details.get("struct", {}).get("title", "N/A")
    method = details.get("exptl", [{}])[0].get("method", "N/A")
    resolution = details.get("rcsb_entry_info", {}).get("resolution_combined", ["N/A"])[0]
    print(f"{pdb_id}: {title}")
    print(f"  Method: {method}, Resolution: {resolution} Å")
```

## Common Methods

- `X-RAY DIFFRACTION` — crystal structures
- `ELECTRON MICROSCOPY` — cryo-EM
- `SOLUTION NMR` — NMR in solution

## Follow-up Suggestions

- "Want me to download this structure and analyze binding sites?"
- "Should I compare with the AlphaFold prediction?"
- "Want me to find ligands bound in this structure?"


---
Source attribution: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: Runchuan-BU
Original project: https://github.com/Runchuan-BU/BioClaw
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Development & Engineering, Education & Research
Roles: Data Scientist, ML / AI Engineer, Researcher
Specialties: API, Cross Platform
Tools: Rcsb Pdb
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 8ee69722c8f386c83d40b2f6e53fbc600fc09a48da813f1ab50502471ff4825c