# RCSB PDB MCP > RCSB PDB connects your AI agent directly to the Protein Data Bank (PDB), the world's primary source for 3D molecular structures. You search and retrieve experimental data on proteins, DNA, and RNA—everything from specific protein-ligand complexes to general structural metadata. Use it to find high-resolution structures by name, method (X-ray, Cryo-EM, NMR), or bound molecule ID. It cuts out the manual database browsing required for structural biology research. ## Overview - **Category:** the-unthinkable - **Price:** Free - **Tags:** bioinformatics, protein-structure, molecular-biology, genomics, data-repository, research-tools ## Description You're connecting your AI agent straight into **RCSB PDB**, the biggest deal for 3D molecular structures. This isn't some flimsy database; it's the global hub where researchers dump all their experimental data on proteins, DNA, and RNA. If you gotta look up how big a molecule is or what kinda complex structure it forms, this tool set gets you there without having to manually click through twenty layers of menus. **`search_pdb`** lets you search the entire Protein Data Bank—we're talking over 220,000 entries here. You don't just get a list; you can identify molecular structures by criteria like the experimental method used (was it X-ray Diffraction? Cryo-EM?), or what resolution was achieved. When you run this search, the results spit out key metadata: the protein or nucleic acid name and function, the precise resolution number, the associated authors, and when they dropped the data. It's perfect for comparing structures; you can pull data points—like resolution and method—across multiple entries to compare molecular architecture on the fly. The search results also specifically list any bound molecules or cofactors, so if you gotta know what ligand is attached, it shows up right there in the metadata. If you already know exactly which structure you're looking at, **`get_pdb_structure`** is your shortcut. You just drop a 4-character PDB ID—like '1HHO' or whatever's on your list—and it pulls the complete structural record instantly. This tool retrieves all the granular details: everything from polymer chain counts to specific cofactor binding sites. When you use these tools, your agent reads deep into the molecular data. You can find structures by name, method, or even by a bound molecule's ID. It bypasses all that tedious database browsing and gives you raw structural facts immediately. ## Tools ### get_pdb_structure PDB IDs are 4-character codes. This tool retrieves all structural details for a known PDB ID. ### search_pdb Searches the Protein Data Bank across 220K+ structures, returning key metadata like method, resolution, and ligands. ## Prompt Examples **Prompt:** ``` Show me the structure of the SARS-CoV-2 main protease. ``` **Response:** ``` 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 ``` **Prompt:** ``` Get full structural details for PDB entry 1HHO — what protein is it? ``` **Response:** ``` 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. ``` **Prompt:** ``` Find all cryo-EM structures of ribosome complexes. ``` **Response:** ``` 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. ``` ## Capabilities ### Identify molecular structures by criteria You search the entire database for molecules matching specific properties like method, resolution, or bound ligand. ### Extract full structural records The tool retrieves complete metadata and details for any known 4-character PDB ID. ### Compare protein structures You gather data points (resolution, method) across multiple entries to compare molecular architecture. ### Determine ligand binding details The search results specifically list bound molecules and their associated structural context. ## Use Cases ### Evaluating a novel drug target's structure A chemist knows the protein name but not its ID. They ask their agent, which runs `search_pdb` to find candidates matching 'kinase inhibitor'. The results narrow down potential targets and provide crucial metadata like resolution (e.g., 2.5 Å) for assessing data quality. ### Checking a specific structure's details A student is given PDB ID '1HHO'. They use `get_pdb_structure` to instantly pull all structural information, verifying it’s deoxy human hemoglobin and seeing the method (X-ray Diffraction) and resolution. ### Comparing multiple reaction mechanisms A researcher needs structures from different sources. They use `search_pdb` to find all Cryo-EM entries related to 'ribosome complexes,' allowing them to compare the molecular machine's structure across various experimental conditions. ### Validating binding site information A biophysicist wants to know if a specific ligand (e.g., N3) was found in high-resolution studies. They use `search_pdb` and filter by 'bound ligands' to quickly identify relevant PDB entries. ## Benefits - Saves time on metadata checks. Instead of visiting multiple database tabs, `search_pdb` gives you one summary record listing the method, resolution, and authors right away. - Directly access complex structures. Use `get_pdb_structure` with a 4-character PDB ID (like 6LU7) to pull full data on everything from cofactors to polymer chains. - Focuses drug design efforts. You find protein-ligand complexes specifically by searching, bypassing general searches and getting right to the structural details needed for virtual screening. - Handles diverse molecular types. The server supports search across proteins, DNA, and RNA structures, making it useful regardless of your macromolecule focus. - Bypasses API key issues. You start searching immediately without needing to manage or generate external API keys. ## How It Works The bottom line is: You query by criteria first, then retrieve the deep data point using the ID provided in the results. 1. Send a query specifying what you need (e.g., 'Find all Cryo-EM structures of ribosomes'). 2. The agent uses `search_pdb` to narrow the search, returning relevant PDB IDs and summarizing their key characteristics. 3. If results are found, or if you provide an ID, the system executes `get_pdb_structure` to pull the full, deep-dive record for that specific entry. ## Frequently Asked Questions **How do I find structures using the RCSB PDB MCP Server?** Use `search_pdb`. You need to tell it criteria like 'protein name,' 'method,' or 'ligand' so it can search the 220K+ entries and give you relevant IDs. **What is the difference between using get_pdb_structure vs search_pdb?** `search_pdb` finds candidates based on criteria. `get_pdb_structure` requires a specific, known 4-character PDB ID and pulls the full record for that single entry. **Can I find structures for DNA or RNA?** Yes. The server supports searching across proteins, DNA, and RNA molecules; you just need to include the type in your query when using `search_pdb`. **Does RCSB PDB MCP Server require an API key?** No. You can start querying molecular structures immediately without needing to manage or generate any API keys. **When I use `get_pdb_structure`, what metadata does it provide about experimental resolution?** The tool provides the exact recorded resolution (e.g., 2.16 Å) alongside the structural details. This metric tells you the precision of the original physical measurement, which is crucial when comparing different structures. **If I use `search_pdb` with a very broad query, how can I optimize the search for speed?** To keep things fast, always narrow your criteria by including restrictive filters first. Combining specific methods (like Cryo-EM) or known ligands dramatically reduces the dataset from 220K+ entries. **What happens when `get_pdb_structure` is called with a PDB ID that doesn't exist?** The system returns an explicit error stating the PDB ID was not found. Your AI client can catch this specific failure and prompt you to re-check the 4-character code or adjust your search parameters. **When using `search_pdb`, how do I ensure I only find protein-ligand co-crystal structures?** You must include 'bound ligand' or 'complex structure' in the tool's criteria. The resulting data will list the associated ligands and their binding site details, confirming a complex structure. **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.