Protein Data Bank

What is protein data bank(PDB)?

The PDB archive is a repository of atomic coordinates and other information describing protein and other important biological macromolecules. Structural biologists use methods such as  X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB.

 Some of the example of protein:

1.	Prolyl oligopeptidase
2.	Thermolysin
3.	Oligopeptidase
4.	Signal peptidase
5.	Collagenase

1. Prolyl oligopeptidase

Prolyl peptidase is a large cytosolic enzyme that belongs to a distinct class of serine peptidase. It also known as prolyl endopeptidase or post-proline cleaving enzyme that in human is encoded by PREP genes. The enzyme is involved in the maturation and degradation of peptide hormons and neuropeptide. Prolyl oligopeptidase is a cytosolic that cleave peptide bonds on the C terminal side of prolyl residues within peptides that are up to approximately 30 amino acids long.

Here

2. Thermolysin

Thermolysin is a thermostable neutral metalloproteinase enzyme produces by the Gram positive bacteria. Thermolysin specifically catalyze the hydrolysis of peptide bonds containing hydrophobic amino acids. It overall structure consist of two roughly spherical domains with a deep cleft running across the middle of molecule separating the two domains. 

http://www.rcsb.org/pdb/explore/explore.do?structureId=1TLX

3.Oligopeptidase 

Oligopeptidase is a enzyme that cleaves peptide but not protein, a property that is due to its structure, the active site of this enzyme is located at the end of a narrow cavity which can only be reached by peptides. It is predominantly smaller than 30 amino acids in length, plays essential role as hormones, against pathogens and neurological activities. 

http://www.rcsb.org/pdb/explore/explore.do?structureId=3AHM

4. Signal peptidase 

Signal peptidase are enzyme that convert secretory and some membrane proteins to their mature forms by cleaving their signal peptides from their N-terminals. The active sites that endoproteolytically cleaves signal peptides from translocated precursor protein is located at the extracytoplasmic site of the membrane.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1T7D

5. Collagenase

Collagenase are enzyme that break the peptide bonds in collagen. They assist in destroying extracellular structure in pathogenesis of bacteria. Collagen are key component of the animal extracellular matrix is made through cleavage of procollagen by collagenase once it has been secreted from the cells.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1PEX