PDB MCP Server

MIT License

Overview InspectNew Schema Related Servers Reviews Score

download_structure

Retrieve atomic structure coordinates from the Protein Data Bank in formats like PDB, mmCIF, MMTF, or XML. Specify PDB ID, format, and optional assembly ID to download.

Instructions

Download structure coordinates in various formats

Input Schema

Name	Required	Description
`assembly_id`	No	Biological assembly ID (optional)
`format`	No	File format (default: pdb)
`pdb_id`	Yes	PDB ID (4-character code)

Input Schema (JSON Schema)

{
  "properties": {
    "assembly_id": {
      "description": "Biological assembly ID (optional)",
      "type": "string"
    },
    "format": {
      "description": "File format (default: pdb)",
      "enum": [
        "pdb",
        "mmcif",
        "mmtf",
        "xml"
      ],
      "type": "string"
    },
    "pdb_id": {
      "description": "PDB ID (4-character code)",
      "type": "string"
    }
  },
  "required": [
    "pdb_id"
  ],
  "type": "object"
}

Install Server

HTTP connection URL

Other Tools from PDB MCP Server

Related Tools

get_structure_info
@Augmented-Nature/PDB-MCP-Server
bc_get_alphafold_info_by_protein_symbol
@biocontext-ai/knowledgebase-mcp
get_protein_structure
@Augmented-Nature/UniProt-MCP-Server
search_structures
@Augmented-Nature/PDB-MCP-Server
search_by_uniprot
@Augmented-Nature/PDB-MCP-Server
download_structure
@Augmented-Nature/AlphaFold-MCP-Server

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/Augmented-Nature/PDB-MCP-Server'

If you have feedback or need assistance with the MCP directory API, please join our Discord server