@pipeworx/rcsb-pdb

Connect: https://gateway.pipeworx.io/rcsb-pdb/mcp · Install: one-click buttons

Tools: 6

RCSB Protein Data Bank MCP — 3-D structure metadata for ~225 k experimentally determined macromolecules. Keyless.

Tools

• search(query, return_type?, limit?) — text search across PDB
• structure(pdb_id) — full entry record (experiment, ligands, polymer entities)
• polymer_entity(pdb_id, entity_id) — single polymer entity (chain) metadata
• ligand(pdb_id, ligand_id) — ligand record
• assembly(pdb_id, assembly_id?) — biological assembly
• summary(pdb_id) — short summary view

Data sources

• Search: https://search.rcsb.org/rcsbsearch/v2/query
• Data: https://data.rcsb.org/rest/v1/core/

Tools

• search — “Find protein structure of [target]” / “search PDB for [protein]” / “is there a crystal structure of [X]” / “[disease target] structures” / “CRISPR / kinase / GPCR structures” — text search the RCSB P
• structure — “PDB entry [1abc] details” / “fetch protein structure [pdb_id]” / “metadata for [PDB ID]” — full PDB entry record by ID (e.g. “1abc”, “7BV2”). Returns experimental method (X-ray / cryo-EM / NMR), reso
• polymer_entity — “Chain [N] of PDB [ID]” / “sequence of chain in [pdb_id]” — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-referen
• ligand — “Ligand / cofactor / drug bound to [pdb_id]” / “small molecule in [PDB entry]” — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what’s
• assembly — “Biological assembly of [pdb_id]” / “functional oligomer for [PDB entry]” — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric
• summary — Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without