get_structure_info

Retrieve detailed structural data for a specific protein or nucleic acid from the Protein Data Bank using its PDB ID.

Instructions

Get detailed information for a specific PDB structure

Input Schema

TableJSON Schema

Name	Required	Description	Default
`pdb_id`	Yes	PDB ID (4-character code, e.g., 1ABC)
`format`	No	Output format (default: json)

Implementation Reference

src/index.ts:429-475 (handler)

Executes the 'get_structure_info' tool: validates input, fetches PDB structure data from RCSB API in specified format (JSON or file), handles errors.

private async handleGetStructureInfo(args: any) {
  if (!isValidPDBIdArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid PDB ID arguments');
  }

  try {
    const pdbId = args.pdb_id.toLowerCase();
    const format = args.format || 'json';

    if (format === 'json') {
      const response = await this.apiClient.get(`/core/entry/${pdbId}`);
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } else {
      // Handle file format downloads
      const baseUrl = 'https://files.rcsb.org/download';
      const extension = format === 'mmcif' ? 'cif' : format;
      const url = `${baseUrl}/${pdbId}.${extension}`;

      const response = await axios.get(url);
      return {
        content: [
          {
            type: 'text',
            text: response.data,
          },
        ],
      };
    }
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching structure info: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:256-267 (registration)

Registers the 'get_structure_info' tool in ListTools response with name, description, and input schema.

{
  name: 'get_structure_info',
  description: 'Get detailed information for a specific PDB structure',
  inputSchema: {
    type: 'object',
    properties: {
      pdb_id: { type: 'string', description: 'PDB ID (4-character code, e.g., 1ABC)' },
      format: { type: 'string', enum: ['json', 'pdb', 'mmcif', 'xml'], description: 'Output format (default: json)' },
    },
    required: ['pdb_id'],
  },
},

src/index.ts:313-314 (registration)
Dispatches tool calls for 'get_structure_info' to the handler in CallToolRequestSchema handler.
```
case 'get_structure_info':
  return this.handleGetStructureInfo(args);
```

src/index.ts:38-48 (helper)

Helper function to validate input arguments for the 'get_structure_info' tool (PDB ID format and optional format).

const isValidPDBIdArgs = (
  args: any
): args is { pdb_id: string; format?: 'json' | 'pdb' | 'mmcif' | 'xml' } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.pdb_id === 'string' &&
    args.pdb_id.length === 4 &&
    /^[0-9][a-zA-Z0-9]{3}$/i.test(args.pdb_id) &&
    (args.format === undefined || ['json', 'pdb', 'mmcif', 'xml'].includes(args.format))
  );

PDB MCP Server