What experimental methods are represented in the PDB?

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.

Do I need authentication to access PDB data?

No. RCSB PDB is completely free and open — funded by NSF, NIH, DOE, and international partners. All 220K+ structures are openly accessible without any registration or API key. The data is licensed under CC0 (public domain).

What information does each PDB entry contain?

Each entry includes: PDB ID (4-character code), structure title, depositing authors, experimental method, resolution in Ångströms, source organism, release date, number of polymer chains, and bound non-polymer ligands (drugs, cofactors, ions). Higher resolution (lower number) means more precise atomic coordinates.

RCSB PDB MCP Server

Name: RCSB PDB
Availability: InStock
Author: Vinkius

rcsb.org

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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.

Vinkius AI Gateway supports streamable HTTP and SSE.

Works with every AI agent you already use

…and any MCP-compatible client

RCSB PDB MCP Server: see your AI Agent in action

AI Agent→Vinkius→RCSB PDB

You

Vinkius AI Gateway

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Built-in capabilities (2)

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

What this connector unlocks

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

Frequently asked questions

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