Biochemistry Archive MCP Server

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get_structure

Retrieve a single PDB entry by ID with named and described bound ligands to inspect a specific candidate after listing structures.

Instructions

One PDB entry with its bound ligands named and described. Use after get_structures to inspect a specific candidate.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "pdb_id": "<pdb_id>"
    },
    "name": "get_structure"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_id`	Yes	Four-character PDB id, e.g. '6LU7'

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Nov 5, 2026

TDQS

A3.8/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the disclosure burden. It does add output context by promising ligand names and descriptions, and it is clearly a read operation by nature, but it says nothing about behavior on an invalid or obsolete PDB id, completeness of the record, or any rate limiting.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two short sentences, zero filler, with the resource definition front-loaded before the sequencing hint. Nothing could be removed without losing information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

A one-parameter read tool with an output schema and full schema coverage needs little prose, and the description supplies purpose plus placement in the workflow. Only the lack of any failure-mode hint keeps it below the top mark.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% and the single pdb_id parameter is documented with a concrete format example ('6LU7'). The description adds no further meaning beyond implying that the id selects the entry, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific resource — one PDB entry plus its bound ligands, named and described — which reads as a retrieval operation. It is distinguishable from the plural sibling get_structures and from find_ligands, though the verb itself is implicit rather than stated.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explicitly routes the agent: 'Use after get_structures to inspect a specific candidate,' which names the prerequisite and the alternative flow. It does not cover when-not-to-use or whether a lighter sibling (e.g., find_ligands) suffices, so it stops short of full coverage.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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