A significant number of proteins require one or more metal ions to be able to carry out their biological function in cells. Consequently, the analysis of interactions of metals with biological macromolecules is an important aspect of structural biology.
Starting from the structural information contained in the Protein Data Bank (PDB), MetalPDB supports the structural analysis of biological macromolecules by providing information on the geometric properties of the metal sites identified in 3D structures.
A unique feature of MetalPDB is that, for each metal site, it identifies structurally similar or equivalent sites occurring in other PDB structures, providing a single reference point to obtain an overview of the occurrence and variability of a given metal site structure across different biological systems, enabling the investigation of questions such as how common a metal site structure is within the same protein family and what variants are known.
- Andreini, C., Cavallaro, G., Rosato, A., Valasatava, Y. (2013) MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids. Journal of Chemical Information and Modeling, issue 53, Volume 11 (Open Access) doi:10.1021/ci400459w
- Use case 'Integrating structural data'