Which Structure Data Is Available on PDB?


Larry Thompson

Which Structure Data Is Available on PDB?

The Protein Data Bank (PDB) is a vast repository of structural information about proteins, nucleic acids, and complex biological assemblies. It serves as a valuable resource for researchers and scientists across the globe. In this article, we will explore the various types of structural data available on the PDB.

Protein Structures

Protein structures form a significant portion of the data in the PDB. These structures provide insights into the three-dimensional organization of proteins, allowing us to understand their functions and interactions with other molecules. The PDB contains structures determined using techniques such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy.

X-ray Crystallography

X-ray crystallography is one of the most commonly used methods to determine protein structures. It involves growing crystals of purified proteins and then bombarding them with X-rays.

The resulting diffraction pattern provides information about the arrangement of atoms in the protein. The PDB houses an extensive collection of protein structures determined using X-ray crystallography.

Nuclear Magnetic Resonance (NMR) Spectroscopy

NMR spectroscopy is another powerful technique for studying protein structures. Unlike X-ray crystallography, NMR spectroscopy can provide insights into protein dynamics and flexibility.

NMR experiments involve measuring the interactions between atomic nuclei in a magnetic field. The PDB contains NMR-derived structures that capture different conformations adopted by proteins.

Nucleic Acid Structures

In addition to proteins, the PDB also hosts a significant amount of nucleic acid structures. These structures reveal the spatial arrangement of DNA and RNA molecules, shedding light on their functions in biological processes.

Double Helical DNA

Double helical DNA structures are crucial for understanding how genetic information is stored and transmitted. The PDB contains numerous DNA structures, including those with modified bases or bound to proteins.

RNA Structures

RNA structures play diverse roles in gene expression and regulation. The PDB offers a wealth of information on RNA structures, including those involved in crucial biological processes like translation and splicing.

Complex Biological Assemblies

The PDB also houses complex biological assemblies. These include protein complexes, virus particles, and other macromolecular assemblies that play critical roles in cellular processes.

Protein-Protein Interactions

The PDB provides insights into the interactions between different proteins. Understanding protein-protein interactions is essential for unraveling signaling pathways, drug discovery, and designing therapeutics.

Virus Structures

The PDB contains a vast collection of virus structures. These structures are invaluable for studying viral replication mechanisms and developing antiviral treatments.

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In conclusion, the Protein Data Bank (PDB) offers a rich collection of structural data, including protein and nucleic acid structures, as well as complex biological assemblies. The availability of these diverse structures makes the PDB an invaluable resource for researchers in various fields, contributing to our understanding of biological processes and aiding in drug discovery and development.

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