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)) ); };