Protein Data Bank...........
A Storage of Macromolecular Structure



Assalamualaikum...hi,guys..!!

  Praise be To Allah we are able to meet again..Today,we would like to introduce you something related to bank...BANK???????...yes..it is about a bank..a place to keep money safe,right??..haha..but not for this bank,this bank only for keeping or saving macromolecular structure..need more explanation??

  Okay,then,we will explain..this bank is known as Protein Data Bank (PDB).The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). 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 via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.


Then,we proceed to the next topic which is Rasmol...Haaaaaaaaaa????
What is Rasmol??

  RasMol is quite related to PDB. RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.


Let's see some example here :

Molecule Name	PBD ID	Structure in RasMol
ClpP	1YG6	ClpP is a self-compartmentalized proteolytic assembly comprised of two, stacked, heptameric rings that, when associated with its cognate hexameric ATPase (ClpA or ClpX), form the ClpAP and ClpXP ATP-dependent protease, respectively. The symmetry mismatch is an absolute feature of this large energy-dependent protease and also of the proteasome, which shares a similar barrel-shaped architecture, but how it is accommodated within the complex has yet to be understood, despite recent structural investigations, due in part to the conformational lability of the N-termini.
HtrA	2L97	High-temperature requirement A (HtrA), a highly conserved family of serine protease, plays crucial roles in protein quality control in prokaryotes and eukaryotes. The HtrA protein contains a C-terminal PDZ domain that mediates the proteolytic activity.
Thermolysin	3FLF	Thermolysin is a thermostable neutral metalloproteinase enzyme produced by the gram-positive bacteria Bacillus thermoproteolyticus. It requires one zinc ion for enzyme activity and four calcium ions for structural stability.Thermolysin specifically catalyzes the hydrolysis of peptide bonds containing hydrophobic amino acids.
Trypsin	4PTI	Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins.Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when either is followed by proline. It is used for numerous biotechnological processes.
LEXA	1JHF	LexA is a repressor enzyme that represses SOS response genes coding for DNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a process called autoproteolysis.

To view and setting the PDB file (the structure picture), you should have RasMol application. The application can be downloaded here.