InterMetalDB

InterMetalDB aggregates structural data on intermolecular metal binding sites within macromolecules to enable analysis of metal-mediated assembly and interactions using structures from the Protein Data Bank (PDB).

Key Features:

• Data source: Structural entries derived from the Protein Data Bank (PDB).
• Data aggregation: Aggregates and annotates interfacial metal binding sites relevant to macromolecular complex assembly.
• Clustering criteria: Clusters interfacial binding sites based on ≥50% sequence similarity and proximity within a 5 Å radius of the nearest metal environment.
• Query logic: Supports construction of queries using logical AND connections between questions for complex searches.
• Filtering options: Filters include structure resolution, description, deposition date, coordinated metal ion type, number of bound amino acid residues, coordination sphere, and other relevant features.
• Updates: Database content is regularly updated.

Scientific Applications:

• Metalloprotein analysis: Enables comparative analysis of metal coordination environments across metalloproteins.
• Protein engineering: Informs design and modification of proteins by revealing metal-mediated interface geometries and coordinating residues.
• Oligomerization studies: Supports investigation of metal-driven oligomerization and assembly mechanisms in macromolecular complexes.
• Structural basis of metal involvement: Facilitates exploration of how metal ions contribute to the formation and stability of biological assemblies.

Methodology:

Interfacial binding sites are clustered by sequence similarity (≥50%) and spatial proximity to metal ions or clusters (within a 5 Å radius of the nearest metal environment).