PDB Entry Molecules: Chains, Sequences, Ligands and Source Organisms of a Structure (PDBe)

pdbe/entry-molecules

Every molecule (entity) in one Protein Data Bank entry by its four-character PDB id: polymers with amino acid or nucleotide sequence, length, weight, chains, gene name and source organism, bound ligands with formula and known synonyms, and waters. Returned as the PDBe response, keyed by the PDB id. Protein Data Bank in Europe data (PDB archive data is CC0), served by Eden Engine; not an official PDBe product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.

Data source

Protein Data Bank in Europe (PDBe), EMBL-EBI

Data from the Protein Data Bank in Europe (PDBe), EMBL-EBI. PDB archive data is CC0 1.0 (wwpdb.org/about/usage-policies); PDBe-added annotation is CC BY 4.0. Served by Eden Engine; not an official PDBe product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

Connect once and your AI can find and run this tool, and any other it needs.

Install it Create an account

agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "pdbe/entry-molecules" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "pdbe/entry-molecules" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "pdbe/entry-molecules", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "pdbe/entry-molecules", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "pdb_id"
  ],
  "properties": {
    "pdb_id": {
      "type": "string",
      "pattern": "^[0-9][a-z0-9]{3}$",
      "description": "Four-character PDB id in lowercase: a digit followed by three lowercase letters or digits, for example 1cbs."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "description": "The PDBe response, keyed by the lowercase PDB id you asked for. The value is a list with one record per molecule (entity).",
  "minProperties": 1,
  "additionalProperties": {
    "type": "array",
    "items": {
      "type": "object",
      "properties": {
        "length": {
          "type": [
            "integer",
            "null"
          ],
          "description": "Residue count, present for polymers."
        },
        "source": {
          "type": "array",
          "items": {
            "type": "object",
            "additionalProperties": true
          },
          "description": "Source organism and expression host of a polymer."
        },
        "weight": {
          "type": [
            "number",
            "null"
          ]
        },
        "synonym": {
          "type": [
            "string",
            "null"
          ]
        },
        "sequence": {
          "type": [
            "string",
            "null"
          ],
          "description": "Polymer sequence, present for polymers."
        },
        "ca_p_only": {
          "type": "boolean"
        },
        "entity_id": {
          "type": "integer"
        },
        "gene_name": {
          "type": [
            "array",
            "null"
          ],
          "items": {
            "type": "string"
          }
        },
        "in_chains": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "pdb_sequence": {
          "type": [
            "string",
            "null"
          ]
        },
        "bound_details": {
          "type": "array",
          "items": {
            "type": "object",
            "additionalProperties": true
          },
          "description": "For a ligand: chemical component id, formula and synonyms."
        },
        "chem_comp_ids": {
          "type": [
            "array",
            "null"
          ],
          "items": {
            "type": "string"
          }
        },
        "molecule_name": {
          "type": [
            "array",
            "null"
          ],
          "items": {
            "type": "string"
          }
        },
        "molecule_type": {
          "type": "string",
          "description": "For example polypeptide(L), bound (a ligand) or water."
        },
        "mutation_flag": {
          "type": [
            "string",
            "null"
          ]
        },
        "in_struct_asyms": {
          "type": "array",
          "items": {
            "type": "string"
          }
        },
        "number_of_copies": {
          "type": "integer"
        },
        "sample_preparation": {
          "type": [
            "string",
            "null"
          ]
        },
        "pdb_sequence_indices_with_multiple_residues": {
          "type": "object",
          "additionalProperties": true
        }
      },
      "additionalProperties": true
    }
  }
}