get_protein_structure

Retrieve 3D protein structure information from PDB references using a UniProt accession number to visualize molecular architecture.

Instructions

Retrieve 3D structure information from PDB references

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1178-1217 (handler)

The handler function for 'get_protein_structure' tool. Fetches UniProt protein data and extracts PDB cross-references, structural features, and subunit comments.

private async handleGetProteinStructure(args: any) {
  if (!isValidProteinInfoArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid protein structure arguments');
  }

  try {
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format: 'json' },
    });

    const protein = response.data;
    const structureInfo = {
      accession: protein.primaryAccession,
      pdbReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'PDB') || [],
      structuralFeatures: protein.features?.filter((f: any) =>
        ['Secondary structure', 'Turn', 'Helix', 'Beta strand'].includes(f.type)
      ) || [],
      structuralComments: protein.comments?.filter((c: any) => c.commentType === 'SUBUNIT') || [],
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(structureInfo, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching protein structure: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:512-522 (schema)

Input schema for the 'get_protein_structure' tool, defining the required 'accession' parameter.

// Structure & Function Analysis Tools
{
  name: 'get_protein_structure',
  description: 'Retrieve 3D structure information from PDB references',
  inputSchema: {
    type: 'object',
    properties: {
      accession: { type: 'string', description: 'UniProt accession number' },
    },
    required: ['accession'],
  },

src/index.ts:748-749 (registration)
Registration of the tool handler in the CallToolRequestSchema switch statement.
```
case 'get_protein_structure':
  return this.handleGetProteinStructure(args);
```

src/index.ts:79-89 (helper)

Helper validation function used by 'get_protein_structure' to validate input arguments.

const isValidProteinInfoArgs = (
  args: any
): args is { accession: string; format?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.accession === 'string' &&
    args.accession.length > 0 &&
    (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format))
  );
};

UniProt MCP Server