PROTEIN
DATA BANK (PDB)
Introduction
The
Protein Data Bank (PDB) is a repository for the three-dimensional structural
data of large biological molecules, such as proteins and nucleic acids. 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.
The
PDB is a key resource in areas of structural biology, such as structural
genomics. Most major scientific journals, and some funding agencies, now
require scientists 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
(i.e., secondary) databases that categorize the data differently. For example,
both SCOP and CATH categorize structures according to type of structure and
assumed evolutionary relations; GO categorize structures based on genes.
RASMOL
RasMol is
a computer program written for molecular graphics visualization
intended and used primarily for the depiction and exploration ofbiological
macromolecule structures, such as those found in the Protein Data Bank. It
was originally developed by Roger Sayle in the early 90s.
Historically,
it was an important tool for molecular biologists since the extremely optimized
program allowed the software to run on (then) modestly powerful personal
computers. Before RasMol, visualization software ran on graphics workstations
that, due to their expense, were less accessible to scholars. RasMol has become
an important educational tool as well as continuing to be an important tool for
research in structural biology.
RasMol
has a complex version history. Starting with the series of 2.7
versions , RasMol is licensed under a dual
license (GPL or custom license RASLIC).
RasMol
includes a language (for selecting certain protein chains,
or changing colors etc.). Jmol and Sirius has incorporated
the RasMol scripting language into its commands.
Protein
Databank (PDB) files can be downloaded for visualization from members of
the Worldwide Protein Data Bank (wwPDB). These have been uploaded by
researchers who have characterized the structure of molecules usually
by X-ray crystallography, NMR spectroscopy orelectron
microscopy.
for more information about rasmol you can click here
No.
|
Name
|
Structure
|
Description
|
1
|
Renin
|  |
We have found that both enantiomeric configurations of the 6-alkoxymethyl-1-aryl-2-piperazinone scaffold display equipotent renin inhibition activity and similar SAR patterns. This enantiomeric flexibility is in contrast to a previously reported 3-alkoxymethyl-4-arylpiperidine scaffold....
|
2
|
Htr A
|  |
Serine protease that cleaves beta-casein/CSN2 as well as several extracellular matrix (ECM) proteoglycans such as decorin/DCN, biglycan/BGN and fibronectin/FN1. Inhibits signaling mediated by TGF-beta family proteins possibly indirectly by degradation of these ECM proteoglycans (By similarity). May act as a tumor suppressor. Negatively regulates, in vitro, trophoblast invasion during placental development and may be involved in the development of the placenta in vivo. May also have a role in ovarian development, granulosa cell differentiation and luteinization.
|
3
|
Subtilisin
|  |
The amino acid composition of subtilisin Novo has been determined. The compositions of all of the 14 expected tryptic peptides from subtilisin Novo were obtained or deduced. A total of 281 residues was found by analysis of the protein, in good agreement with the total of 275 residues in the expected 14 tryptic peptides. The amino acid compositions and peptide maps of the tryptic peptides from subtilisin Novo and subtilisin BPN' were identical. It is concluded that the proteins are probably identical.
|
4
|
DegQ
|  |
DegQ could degrade transiently denatured and unfolded proteins which accumulate in the periplasm following stress conditions. DegQ is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for a beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable to be cleaved, thereby preventing non-specific proteolysis of folded proteins. DegQ can substitute for the periplasmic protease DegP.
|
5
|
thermolysin
|  |
Thermolysin (EC 3.4.24.27, Bacillus thermoproteolyticus neutral proteinase, thermoase, thermoase Y10, TLN) is a thermostable neutralmetalloproteinase 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. However thermolysin is also widely used for peptide bond formation through the reverse reaction of hydrolysis. Thermolysin is the most stable member of a family of metalloproteinases produced by various Bacillus species. These enzymes are also termed 'neutral' proteinases or thermolysin -like proteinases (TLPs).
|
