PDB Database

Overview

RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across ~260,000 experimentally determined entries (2026-09) plus computed structure models (CSMs) imported from AlphaFold DB and ModelArchive.

Scripts

scripts/query_pdb.py — RCSB Search + Data + file APIs (stdlib only, JSON to stdout):

python scripts/query_pdb.py search hemoglobin --rows 25     # full-text search (entry IDs)
python scripts/query_pdb.py entry 4HHB                      # entry metadata
python scripts/query_pdb.py download 4HHB --format cif      # download coordinates

When to Use This Skill