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Protein Structure Details

science.pdb.structure
Read-onlyIdempotent

Retrieve comprehensive metadata for protein structures by PDB ID: experimental method, resolution, molecular weight, chain composition, and citation details. Supports drug design and structural analysis.

Instructions

Get full details for a 3D protein structure by PDB ID — title, experimental method (X-ray/cryo-EM/NMR), resolution, molecular weight, chain counts (protein/DNA/RNA), deposit date, primary citation with DOI and PubMed ID. Essential for drug design and structural analysis (RCSB PDB)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB identifier (e.g. "4HHB" for hemoglobin, "1BNA" for DNA, "6LU7" for SARS-CoV-2 main protease)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
Behavior4/5

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

Annotations already declare readOnlyHint true, destructiveHint false, idempotentHint true. The description adds value by enumerating the exact fields returned (title, method, resolution, etc.), which is behavioral context beyond annotations.

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?

The description is two sentences, front-loaded with the action and key fields, and the second sentence adds a use case. Every part is necessary and without fluff.

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

Completeness5/5

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

With only one well-documented parameter and an output schema present, the description sufficiently covers the tool's functionality. It tells the agent what to expect and what it returns, leaving no important gaps.

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% with a detailed description for pdb_id including examples. The tool description does not add further parameter semantics beyond what the schema already provides, maintaining the baseline score.

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

Purpose5/5

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

The description explicitly states 'Get full details for a 3D protein structure by PDB ID' and lists specific fields (title, method, resolution, etc.), making the purpose clear and differentiated from sibling tools like science.pdb.ligand or science.pdb.search.

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

Usage Guidelines3/5

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

The description says 'Essential for drug design and structural analysis' but does not explicitly state when not to use or name alternative tools. The context from sibling names helps, but the description itself lacks direct guidance on selection.

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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