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MetalPDB


NAR Molecular Biology Database Collection entry number 1575
Andreini, C.1,2, Cavallaro, G.1, Lorenzini, S.1, and Rosato, A.1,2
1Magnetic Resonance Center (CERM) – University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy

2Department of Chemistry – University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy

Database Description

MetalPDB is a resource aimed at conveying the information available on the three-dimensional structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are three-dimensional templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyze similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. The Search menu of the interface offers various options to interrogate the database, including (i) by PDB code, (ii) by EC Number, (iii) by macromolecule name, (iv) by UniProt id, (v) by metal element, (vi) by performing a BLAST search, and (vii) through an Advanced Query interface. The latter allows users to formulate queries with varying degrees of complexity, by specifying e.g. molecule type (protein, nucleic acid, …), site nuclearity, metal contents, metal geometry. The various conditions set are connected by logical AND operators. Furthermore, the Advanced Query interface allows the results of a query to be downloaded to a file rather than visualized (which is instead the only option available for simple queries). MetalPDB is updated monthly in an automated manner.

Acknowledgements

The technical help of Enrico Morelli is gratefully acknowledged. MetalPDB is supported by MIUR (Ministero Italiano dell’Università e della Ricerca) through the FIRB projects RBFR08WGXT and RBRN07BMCT and the PRIN project 2009FAKHZT.

Subcategory: Nucleic acid structure

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