search_by_uniprot

Find PDB structures linked to a UniProt accession number to analyze protein structures in the Protein Data Bank.

Instructions

Find PDB structures associated with a UniProt accession

Input Schema

TableJSON Schema

Name	Required	Description	Default
`uniprot_id`	Yes	UniProt accession number
`limit`	No	Number of results to return (1-1000, default: 25)

Implementation Reference

src/index.ts:519-566 (handler)

The handler function that executes the search_by_uniprot tool logic. It validates input, constructs a query for RCSB search API using UniProt ID, fetches results, and returns formatted JSON or error.

private async handleSearchByUniprot(args: any) {
  if (!args || typeof args.uniprot_id !== 'string') {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid UniProt search arguments');
  }

  try {
    const searchQuery = {
      query: {
        type: "terminal",
        service: "text",
        parameters: {
          attribute: "rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession",
          operator: "exact_match",
          value: args.uniprot_id
        }
      },
      return_type: "entry",
      request_options: {
        paginate: {
          start: 0,
          rows: args.limit || 25
        },
        results_content_type: ["experimental"]
      }
    };

    const response = await this.rcsb_apiClient.post('/query', searchQuery);

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(response.data, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error searching by UniProt: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:284-291 (schema)

Input schema defining parameters for the search_by_uniprot tool: uniprot_id (required string) and optional limit.

inputSchema: {
  type: 'object',
  properties: {
    uniprot_id: { type: 'string', description: 'UniProt accession number' },
    limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 },
  },
  required: ['uniprot_id'],
},

src/index.ts:281-292 (registration)

Tool registration in the ListTools response, including name, description, and input schema.

{
  name: 'search_by_uniprot',
  description: 'Find PDB structures associated with a UniProt accession',
  inputSchema: {
    type: 'object',
    properties: {
      uniprot_id: { type: 'string', description: 'UniProt accession number' },
      limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 },
    },
    required: ['uniprot_id'],
  },
},

src/index.ts:317-318 (registration)
Dispatch case in CallToolRequest handler that routes to the search_by_uniprot handler function.
```
case 'search_by_uniprot':
  return this.handleSearchByUniprot(args);
```

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