Protein Data Bank

PROTEIN DATA BANK (PDB)

Protein Data Bank (PDB) is a repository for 3-D biological macromolecular structure such as proteins and nucleic acid. The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the internet. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB database is updated weekly every Tuesday. Up until 21 September 2010, there are 68421 structures that exist in the PDB. Table below show the experimental method to show the structures.

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	55480	1231	2605	17	59333
NMR	7512	925	162	7	8606
Electron microscopy	214	17	77	0	308
Hybrid	24	1	1	1	27
Other	126	4	4	13	147
Total:	63356	2178	2849	38	68421

One example that we can take from the Pdb database is the structure of LexA protein. We can search for it in the search box at the top of the page as shown below.

Next, we click at the first type of LexA proteins that come out in the search. Here we can see the description of the LexA protein with it scientific name.

 

We also can download the structure from this page and by using Raswin, we can alter the colour and shape of the structures. For example, below I use the stick for display and group for colour.

 

There are other type of display and colour that we can choose by using Raswin. Anybody who would like to download this program can click here.