Protein Data Bank

A little introduction

Protein Data Bank is a storage site for information and 3d images of biological proteins related macromolecule. It is worldwide, and shared among students and researchers, uploaded into the site and downloadable. One of the site is RCSB Protein Data Bank. The downloaded macromolecules images are opened by using a software like RasWIN, we could get the software from here.

Samples of 5 proteins

LexA

"Repressor LexA or LexA is a repressor enzyme (EC 3.4.21.88) 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." - Wikipedia.org

LEXA G85D MUTANT

"LexA repressor undergoes a self-cleavage reaction. In vivo, this reaction requires an activated form of RecA, but it occurs spontaneously in vitro at high pH. Accordingly, LexA must ...  " Click For More

Type	Code
Molecule	LEXA REPRESSOR
Polymer	1 | Type: Protein | Length: 202
Chain	A, B
EC#	3.4.21.88
Mutation	G85D
Organism	Escheria coli
Gene Name	lexA exrA spr tsl umuA b4043 JW4003
UnitProtKB	Protein Feature View | Search PDB | P0A7C2

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1JHF

Trypsin

"Trypsin (EC 3.4.21.4) 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. The process is commonly referred to as trypsin proteolysis or trypsinisation, and proteins that have been digested/treated with trypsin are said to have been trypsinized." - Wikipedia.org

ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY

Type	Code
Molecule	Trypsin
Polymer	1 | Type: Protein | Length: 223
Chain	A
EC#	3.4.21.4
Mutation	N/A
Organism	Bos Taurus
Gene Name	N/A
UnitProtKB	Protein Feature View | Search PDB | P00760

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=2PTN

HtrA

Crystal Structure of DegP (HtrA)

"Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish ... " Click for more

Type	Code
Molecule	PROTEASE DO
Polymer	1 | Type: Protein | Length: 448
Chain	A, B
EC#	3.4.21.107
Mutation	S210A
Organism	Escherichia Coli
Gene Name	degP htrA ptd b0161 JW0157
UnitProtKB	Protein Feature View | Search PDB | P0C0V0

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1KY9

Pepsin

"Pepsin (from the Greek πέψη, pepsi, meaning digestion) is an enzyme whose zymogen (pepsinogen) is released by the chief cells in the stomach and that degrades food proteins into peptides. It was discovered in 1836 by Theodor Schwann who also coined its name from the Greek word pepsis, meaning digestion (peptein: to digest). It was the first enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. Pepsin is a digestive protease, a member of the aspartate protease family." - Wikipedia

CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3

"The three-dimensional structures of pepsin inhibitor-3 (PI-3) from Ascaris suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed ... " Click for more

Type	Code
Molecule	MAJOR PEPSIN INHIBITOR PI-3
Polymer	1 | Type: Protein | Length: 149
Chain	A
EC#	N/A
Mutation	N/A
Organism	Ascaris Suum
Gene Name	N/A
UnitProtKB	Protein Feature View | Search PDB | P19400

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1F32

Amylase

"Amylase /ˈæmɪleɪz/ is an enzyme that catalyses the breakdown of starch into sugars. Amylase is present in the saliva of humans and some other mammals, where it begins the chemical process of digestion. Foods that contain much starch but little sugar, such as rice and potato, taste slightly sweet as they are chewed because amylase turns some of their starch into sugar in the mouth. The pancreas also makes amylase (alpha amylase) to hydrolyse dietary starch into disaccharides and trisaccharides which are converted by other enzymes to glucose to supply the body with energy. Plants and some bacteria also produce amylase. As diastase, amylase was the first enzyme to be discovered and isolated (by Anselme Payen in 1833). Specific amylase proteins are designated by different Greek letters. All amylases are glycoside hydrolases and act on α-1,4-glycosidic bonds." - Wikipedia

HUMAN SALIVARY AMYLASE

"Salivary alpha-amylase, a major component of human saliva, plays a role in the initial digestion of starch and may be involved in the colonization of bacteria involved ..." Click for more

Type	Code
Molecule	AMYLASE
Polymer	1 | Type: Protein | Length: 496
Chain	A
EC#	3.2.1.1
Mutation	1
Organism	Homo Sapiens
Gene Name	AMY1A AMY1 AMY1B AMY1C
UnitProtKB	Protein Feature View | Search PDB | P04745

or more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1SMD