analyze-active-site
Analyze protein active sites using PDB IDs to identify binding pockets and functional regions for structural biology research.
Instructions
Analyze the active site of a protein structure
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pdbId | Yes | The PDB ID of the protein structure to analyze (e.g., 6LU7) |
Implementation Reference
- src/tools/analyzeActiveSite.ts:92-371 (handler)The main handler function that implements the tool logic: normalizes PDB ID, fetches structure data, binding sites, ligands, residues, and UniProt function info from APIs, then generates a comprehensive text analysis report.
export async function analyzeActiveSite({ pdbId }: { pdbId: string }, extra: RequestHandlerExtra): Promise<CallToolResult> { console.error(`Processing analyze-active-site request for PDB ID: ${pdbId}`); // Normalize PDB ID format (uppercase) pdbId = pdbId.toUpperCase(); // Use REST API to get basic structure data const entryUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}`; const structureData = await makeApiRequest(entryUrl) as StructureData; if (!structureData) { return { content: [ { type: "text", text: `Failed to retrieve structure data for PDB ID: ${pdbId}. Please verify this is a valid PDB ID.`, }, ], }; } // Extract title with fallback options const title = structureData.struct?.title || structureData.struct?.pdbx_descriptor || (structureData.rcsb_primary_citation?.title) || "Unknown protein"; let activeSiteText = `Analysis of ${pdbId}: ${title}\n\n`; // Add structure summary information if (structureData.rcsb_entry_info) { const info = structureData.rcsb_entry_info; activeSiteText += "Structure Summary:\n"; if (info.molecular_weight) { activeSiteText += `Molecular Weight: ${info.molecular_weight.toLocaleString()} Da\n`; } if (info.deposited_polymer_monomer_count) { activeSiteText += `Residue Count: ${info.deposited_polymer_monomer_count.toLocaleString()}\n`; } if (info.deposited_atom_count) { activeSiteText += `Atom Count: ${info.deposited_atom_count.toLocaleString()}\n`; } if (info.polymer_entity_count_protein) { activeSiteText += `Protein Chains: ${info.polymer_entity_count_protein}\n`; } if (info.ligand_count) { activeSiteText += `Ligand Count: ${info.ligand_count}\n`; } activeSiteText += "\n"; } // Get binding site information const structSiteUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/struct_site`; const structSiteData = await makeApiRequest(structSiteUrl) as BindingSite[]; if (structSiteData && Array.isArray(structSiteData) && structSiteData.length > 0) { activeSiteText += "Binding Site Information:\n"; structSiteData.forEach((site: BindingSite, index: number) => { activeSiteText += `Site ${index + 1} (${site.id || site.rcsb_id || "Unknown"}):\n`; if (site.details) { activeSiteText += `Description: ${site.details}\n`; } if (site.pdbx_evidence_code) { activeSiteText += `Evidence: ${site.pdbx_evidence_code}\n`; } if (site.pdbx_site_details) { activeSiteText += `Additional details: ${site.pdbx_site_details}\n`; } activeSiteText += "\n"; }); } else { // Try alternative approach: active site residue information // Check for polymer entities with Uniprot annotations that might have active site information const polymerUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/polymer_entity`; const polymerData = await makeApiRequest(polymerUrl) as PolymerEntity[]; let foundActiveSiteInfo = false; if (polymerData && Array.isArray(polymerData)) { for (const entity of polymerData) { // Check if entity has Uniprot features with active site annotations if (entity.rcsb_polymer_entity_annotation && Array.isArray(entity.rcsb_polymer_entity_annotation)) { const activeSiteAnnotations = entity.rcsb_polymer_entity_annotation.filter( (ann: PolymerEntityAnnotation) => ann.type && (ann.type.toLowerCase().includes('active site') || ann.type.toLowerCase().includes('binding site') || ann.type.toLowerCase().includes('site')) ); if (activeSiteAnnotations.length > 0) { foundActiveSiteInfo = true; activeSiteText += "Active/Binding Site Annotations:\n"; activeSiteAnnotations.forEach((ann: PolymerEntityAnnotation, index: number) => { activeSiteText += `Annotation ${index + 1} (${ann.type || "Unknown"}):\n`; if (ann.description) { activeSiteText += `Description: ${ann.description}\n`; } if (ann.annotation_lineage) { activeSiteText += `Classification: ${ann.annotation_lineage.map((a) => a.name).join(' > ')}\n`; } activeSiteText += "\n"; }); } } } } if (!foundActiveSiteInfo) { activeSiteText += "No binding site information available in the structure data.\n\n"; } } // Get ligand (nonpolymer entity) information const ligandsUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/nonpolymer_entity`; const ligandsData = await makeApiRequest(ligandsUrl) as LigandEntity[]; let foundLigandInfo = false; if (ligandsData && Array.isArray(ligandsData) && ligandsData.length > 0) { foundLigandInfo = true; activeSiteText += "Ligands:\n"; ligandsData.forEach((ligand: LigandEntity) => { const compId = ligand.pdbx_entity_nonpoly?.comp_id || ligand.rcsb_nonpolymer_entity_container_identifiers?.comp_id || "Unknown"; const name = ligand.pdbx_entity_nonpoly?.name || "Unknown"; activeSiteText += `- ${compId}: ${name}\n`; }); activeSiteText += "\n"; } if (!foundLigandInfo) { // Try alternate API endpoint for ligands const alternateLigandsUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/ligands`; const alternateLigandsData = await makeApiRequest(alternateLigandsUrl) as LigandEntity[]; if (alternateLigandsData && Array.isArray(alternateLigandsData) && alternateLigandsData.length > 0) { foundLigandInfo = true; activeSiteText += "Ligands:\n"; alternateLigandsData.forEach((ligand: LigandEntity) => { const compId = ligand.chem_comp_id || "Unknown"; const name = ligand.chem_comp_name || "Unknown"; activeSiteText += `- ${compId}: ${name}\n`; }); activeSiteText += "\n"; } } // Try one more approach - using the PDB chemical component data if (!foundLigandInfo) { const chemCompUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/chem_comp`; const chemCompData = await makeApiRequest(chemCompUrl) as LigandEntity[]; if (chemCompData && Array.isArray(chemCompData) && chemCompData.length > 0) { // Filter out standard amino acids and nucleotides const standardResidues = new Set([ 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'A', 'C', 'G', 'T', 'U', 'DA', 'DC', 'DG', 'DT', 'DU' ]); const ligandComps = chemCompData.filter((comp: LigandEntity) => !standardResidues.has(comp.id || '') && comp.type !== 'POLYMER' && comp.type !== 'AMINO ACID' ); if (ligandComps.length > 0) { foundLigandInfo = true; activeSiteText += "Ligands and Chemical Components:\n"; ligandComps.forEach((comp: LigandEntity) => { activeSiteText += `- ${comp.id}: ${comp.name || 'Unknown'} (${comp.type || 'Unknown type'})\n`; }); activeSiteText += "\n"; } } if (!foundLigandInfo) { activeSiteText += "No ligand information available.\n\n"; } } // Get polymer entity information to extract UniProt IDs const polymerUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/polymer_entity`; const polymerData = await makeApiRequest(polymerUrl) as PolymerEntity[]; // Extract UniProt IDs from polymer entities let uniprotIds: string[] = []; if (polymerData && Array.isArray(polymerData)) { polymerData.forEach((entity: PolymerEntity) => { if (entity.rcsb_polymer_entity_container_identifiers?.uniprot_ids) { uniprotIds = uniprotIds.concat(entity.rcsb_polymer_entity_container_identifiers.uniprot_ids); } }); } // Get UniProt data if available if (uniprotIds.length > 0) { const uniprotId = uniprotIds[0]; const uniprotUrl = `${UNIPROT_API_BASE}/${uniprotId}`; const uniprotData = await makeApiRequest(uniprotUrl) as UniprotData; if (uniprotData) { activeSiteText += `\nProtein Function (from UniProt ${uniprotId}):\n`; try { if (uniprotData.comments) { const functionComments = uniprotData.comments.filter((c) => c.commentType === "FUNCTION") || []; if (functionComments.length > 0 && functionComments[0].texts && functionComments[0].texts.length > 0) { activeSiteText += functionComments[0].texts[0].value; } else { activeSiteText += "No function information available in UniProt."; } } else { activeSiteText += "Function information not available."; } } catch (error) { console.error("Error processing UniProt data:", error); activeSiteText += "Error processing UniProt data."; } activeSiteText += "\n\n"; } } // Get binding site residue details const structSiteResiduesUrl = `${RCSB_PDB_DATA_API}/core/entry/${pdbId}/struct_site_gen`; const siteResiduesData = await makeApiRequest(structSiteResiduesUrl) as SiteResidue[]; if (siteResiduesData && Array.isArray(siteResiduesData) && siteResiduesData.length > 0) { // Group residues by site ID const siteResiduesMap: {[key: string]: SiteResidue[]} = {}; siteResiduesData.forEach((residue: SiteResidue) => { const siteId = residue.site_id || ''; if (!siteResiduesMap[siteId]) { siteResiduesMap[siteId] = []; } siteResiduesMap[siteId].push(residue); }); // Add residue information for each site Object.keys(siteResiduesMap).forEach(siteId => { activeSiteText += `Residues in site ${siteId}:\n`; siteResiduesMap[siteId].forEach((residue: SiteResidue) => { activeSiteText += `- ${residue.label_comp_id || "?"} ${residue.label_seq_id || "?"} (Chain ${residue.label_asym_id || "?"})\n`; }); activeSiteText += "\n"; }); } // Add a link to view the structure in 3D activeSiteText += `View this structure in 3D: https://www.rcsb.org/structure/${pdbId}`; return { content: [ { type: "text", text: activeSiteText, }, ], }; } - src/tools/analyzeActiveSite.ts:85-87 (schema)Input schema using Zod defining the required 'pdbId' parameter as a string.
export const analyzeActiveSiteSchema = { pdbId: z.string().describe("The PDB ID of the protein structure to analyze (e.g., 6LU7)"), }; - src/server/index.ts:27-32 (registration)Registers the tool with the MCP server, providing name, description, schema, and handler function.
server.tool( "analyze-active-site", "Analyze the active site of a protein structure", analyzeActiveSiteSchema, analyzeActiveSite );