pdb

name	pdb
description	3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.
metadata	null

PDB - Protein Data Bank

Search and fetch protein structures from the RCSB Protein Data Bank.

Usage

Search for structures:

python3 {baseDir}/scripts/pdb_search.py --query "kinase human"

Get structure details:

python3 {baseDir}/scripts/pdb_search.py --pdb-id 1ATP

Search by sequence:

python3 {baseDir}/scripts/pdb_search.py --sequence "MTEYKLVVVGAGGVGKSALTIQLIQ" --identity 70

Parameters

Parameter	Description	Default
--query	Text search query	-
--pdb-id	Specific PDB ID to fetch	-
--sequence	Sequence for similarity search	-
--identity	Minimum sequence identity %	90
--max-results	Maximum results	10
--format	Output: summary, detailed, json	summary

Examples

# Search for insulin structures
python3 {baseDir}/scripts/pdb_search.py --query "insulin"

# Get details for a specific structure
python3 {baseDir}/scripts/pdb_search.py --pdb-id 4HHB

# Find structures similar to a sequence
python3 {baseDir}/scripts/pdb_search.py --sequence "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" --identity 50

# Get JSON output
python3 {baseDir}/scripts/pdb_search.py --query "p53 DNA binding" --format json

Output Fields

• PDB ID - 4-character structure identifier
• Title - Structure title
• Resolution - X-ray resolution in Angstroms
• Method - Experimental method (X-RAY, NMR, EM)
• Release Date - When structure was released
• Organism - Source organism
• Chains - Polymer chains in structure

Query Limitations — Read Before Using

PDB stores experimentally determined 3D structures. Queries must target proteins or genes with known deposited structures. Abstract or chemistry-only queries return zero results.

❌ Fails	✅ Works
"BTK covalent inhibitor"	"BTK" or "Bruton tyrosine kinase"
"warhead optimization"	"1K2P" (direct PDB ID)
"ADMET prediction"	"EGFR kinase inhibitor complex"

Tips for avoiding zero results:

• Use short protein names or gene names: "BTK", "p53", "EGFR"
• Use a specific PDB ID (--pdb-id 3K54) when you already have one from UniProt cross-refs
• If zero results, broaden the query — e.g., "kinase" instead of "covalent kinase inhibitor BTK"
• Not all proteins have PDB entries; check UniProt cross-refs first

Notes

• Uses RCSB PDB REST API (no authentication)
• Structures include X-ray, NMR, and cryo-EM
• Resolution shown for X-ray structures
• Links provided to 3D viewers