MCP For Claude Marketplace
RCSB PDB

RCSB PDB MCP Connector for Claude

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Explore 220K+ 3D molecular structures — search proteins, DNA, and RNA by name, experimental method, resolution, and bound ligands from the Protein Data Bank.

2 tools Official Updated Jun 28, 2026 Official Vinkius Partner
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Connect your AI agent to the RCSB Protein Data Bank — the world's repository of experimentally determined 3D structural data for biological macromolecules.

What you can do

  • Structure Search — Find protein, DNA, and RNA structures by name, function, disease association, or organism across 220K+ experimentally determined entries
  • PDB Entry Lookup — Get complete structural details by 4-character PDB ID (e.g., 1HHO for hemoglobin, 6LU7 for SARS-CoV-2 main protease) including experimental method, resolution, and bound molecules

How it works

  1. Subscribe to this server
  2. Start searching molecular structures immediately — no API key required

Who is this for?

  • Structural Biologists — quickly access experimental metadata, resolution, and method details for molecular structures
  • Drug Discovery Teams — find protein-ligand co-crystal structures for structure-based drug design and virtual screening
  • Biochemistry Students — understand protein architecture by exploring real experimental structures with annotations
bioinformaticsprotein-structuremolecular-biologygenomicsdata-repositoryresearch-tools

2 tools expose this connector's capabilities to your AI agent.

get_pdb_structure

PDB IDs are 4-character codes like 1HHO, 6LU7, 7BNN. Get full structural details by PDB ID

search_pdb

Returns PDB ID, title, experimental method (X-ray, Cryo-EM, NMR), resolution, authors, and bound ligands. Essential for drug discovery and structural biology. Search 220K+ 3D molecular structures in the Protein Data Bank

See how to talk to your AI agent using RCSB PDB.

Show me the structure of the SARS-CoV-2 main protease.

Found PDB 6LU7: Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with inhibitor N3. Method: X-ray Diffraction, Resolution: 2.16 Å. Authors: Jin et al. Released: 2020-02-05. Ligands: N3 (peptide-like inhibitor). This was one of the first high-resolution structures of the COVID-19 drug target. View: rcsb.org/structure/6LU7

Get full structural details for PDB entry 1HHO — what protein is it?

PDB 1HHO: Deoxy Human Hemoglobin — the oxygen-carrying protein in red blood cells. Method: X-ray Diffraction, Resolution: 2.10 Å. Authors: Fermi et al. Released: 1984-07-20. Contains 4 polymer chains (2 alpha, 2 beta subunits) with heme (protoporphyrin IX containing iron) bound as cofactor.

Find all cryo-EM structures of ribosome complexes.

Found 10 ribosome structures determined by Cryo-EM. Highlights: Human 80S ribosome (PDB 4UG0) at 3.6 Å resolution — the molecular machine that translates mRNA into proteins. Also found: E. coli 70S ribosome with antibiotics bound (critical for understanding antibiotic mechanisms), and mitochondrial ribosome structures.

The PDB contains structures determined by four main methods: X-ray Crystallography (85% of entries, atomic resolution), Cryo-EM (rapidly growing, now 15%+ of new deposits), NMR Spectroscopy (solution-state structures), and Neutron Diffraction (hydrogen atom positions). Each entry lists its method and resolution.

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