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unip_gen_unipdb_unip_unipdb_unip_acc_bf823946

Read-only

Retrieve PDB structures mapped to a UniProt accession, with sequence, chain coverage, observed regions, mutations, modifications, ligands, and experiment metadata.

Instructions

Retrieve comprehensive information on PDB structures mapped to a given UniProt accession. The response includes the UniProt sequence and length, along with detailed structure annotations such as entity and chain identifiers, residue coverage in UniProt and PDB numbering, observed regions, mutations, modifications, experiment type, resolution, ligand and entity counts, and supporting metadata like titles, ranking scores, and additional structure-specific information. This endpoint provides an integrated view of how PDB structures align with and represent the UniProt sequence

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
uniprot_accessionYesUniProt accession. title: Uniprot Accession description: UniProt accession.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered and the description does not contradict it. The description adds substantial detail about the returned payload (coverage numbering, mutations, resolution, ligand counts), which is genuine behavioral context, but it says nothing about pagination, size limits, or failure modes for an unmapped accession. With annotations carrying the safety burden, a 3 is appropriate.

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

Conciseness3/5

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

The opening sentence is correctly front-loaded, but the response-field enumeration runs long and the closing sentence ('This endpoint provides an integrated view...') merely restates the premise without adding information. The title annotation duplicates this text verbatim, suggesting the field list is padding rather than earned content.

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?

With no output schema, the description must describe return values, and it does so thoroughly — sequence, length, chain identifiers, coverage in both numbering schemes, mutations, resolution, ligand/entity counts, and metadata. An agent knows what it will get back. It is only incomplete in omitting usage boundaries and error behavior.

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 description coverage is 100% for the single parameter, so the baseline is 3. The description mentions 'a given UniProt accession' but adds no format guidance (e.g. accession vs. entry name) beyond what the schema already states, so it neither compensates nor regresses.

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 opens with a specific verb+resource: 'Retrieve comprehensive information on PDB structures mapped to a given UniProt accession.' That is unambiguous about what is returned and from which key. It does not, however, distinguish itself from the many UniProt/PDB sibling endpoints (unip_map, unip_var, unip_giruiru, etc.), so a 4 rather than 5.

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

Usage Guidelines2/5

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

There is no when-to-use guidance, no prerequisites, and no mention of alternative tools despite ~30 siblings operating on UniProt accessions and entity IDs. The agent must infer from the resource name alone that this is the PDB-mapping endpoint rather than the annotations, variants, or interaction endpoints.

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