12.4 Protein Data Bank (PDB)
The Protein Data Bank (PDB) is a freely accessible online database that stores and provides three-dimensional (3D) structural information of large biological molecules. It serves as a critical resource in bioinformatics and molecular biology.
Website: The primary access point is through the Worldwide Protein Data Bank (wwPDB) website: www.wwpdb.org.
Content and Scope
Biomolecules Included: The database contains structural information for a wide range of biomolecules:
- Proteins
- Nucleic acids (DNA and RNA)
- Lipids
- Carbohydrates
Data Stored: For each entry, the PDB provides:
- 3D atomic coordinates of the biomolecule.
- Detailed structural information.
- Experimental data (e.g., from X-ray crystallography, NMR spectroscopy).
- Functional data and annotations.
Scale: The database has grown exponentially since its establishment in 1971 and now contains over 180,000 biomolecule structures. Each structure is assigned a unique identifier known as a PDB ID.
The structures in PDB are determined using experimental methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy.
Management and Importance
Management: The PDB is managed by the Worldwide Protein Data Bank (wwPDB), a consortium of leading research institutions and organizations.
Biological Significance: The PDB is a cornerstone for modern biomolecular research. It is essential for:
- Advancing our understanding of fundamental biological processes at the molecular level.
- Developing innovative treatments and drugs (e.g., drug design based on protein structures).
- Structural bioinformatics and computational biology studies.
The determination of biomolecule structures is important for drug discovery because understanding the 3D structure of target proteins allows researchers to design drugs that fit precisely into active sites and bind effectively, a process known as Rational Drug Design.
Example: Insulin in the PDB
The PDB provides detailed views of biomolecule structures, such as the hormone insulin, allowing researchers to explore its chains, active sites, and overall conformation.
