Protein Database : RCSB Protein Data Bank

PROTEIN DATA BANK

                          Figure 1 : Shows the homepage picture of the Protein Data Bank (PDB)

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecule, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologist and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBi, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank.

 

The PDB  is a key resource in area of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, now require scientist to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived databases that categorize the data differently. For an example, both SCOP and CATH categorize structure according to type of the structure and assumed evolutionary relations.
 

 

         
      Figure 2: Shows the list of information provided for each and every topic regarding protein.

                       Figure 3 : Shows the screen-print of one of the information in the database.

The information that I find interesting in the Protein Data Bank  is regarding the bacteria. There is a term called Bacteriorhodopsin.It actually describes a compact molecular machine which will use the sunlight to pump the protons across the plasma membrane. It was actually built by a halophilic bacteria. Halophilic bacteria is also known as a "salt loving" bacteria.This compact molecular machine usually found in high-temperature brine pools.The main function of it is actually they will use the sunlight to pump the proton outwards across the membrane, whereby making the inside 10,000-fold more alkaline than the outside.Using another type of protein, ATP synthase, building much of the ATP that powers the cell, these protons are allowed to flow back inwards. Bacteriorhodopsin is made up of three  protein chains. It is found embedded in dense arrays in the membranes of the bacteria. At the heart of the each protein chain is a molecule of retinal, which is bound deep inside the protein and connected through a lysine amino acid.

By capturing of the light, the bacteriorhodopsin could build four different types of rhodopsins. Rhodopsin is also a pump that funnels chloride ions instead of protons. Apart from that it is also function as keeping the internal concentration of chloride at high that match the salty condition outside the ce