PDB

Protein Data Bank

l A repository for 3-D biological macromolecular

structure

l All data are available to the public

l It includes proteins, nucleic acids and viruses

l Obtained by X-Ray crystallography (80%) or

NMR spectroscopy (16%)

l Submitted by biologists and biochemists from

around the world

l PDB is an important resource for research in the

academic, pharmaceutical, and biotechnology

sectors

l Examples

– Will this molecule turns into a cancer cell?

– Can this combination of molecules cure common cold?

– How does radiation affect the RNA and DNA?

PDB data

l Information required includes

– Coordinates of all the atoms

– Chemical description of the various molecules

in the crystal

– Experimental information about the structure

– Structural description of the biological molecule

Software Tools

l Various software tools can minimize the

amount of manual labor

l Help scientists deposit their results quicker

l Also help validate their results

l Commonly used software:

– pdb_extract

– ADIT

– PDB Validation Suite

Some examples :

 

 

Trypsin(STRUCTURE OF FORM III CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR)

Classification:	Proteinase Inhibitor (trypsin)
Structure Weight:	6622.57

Molecule:

PANCREATIC TRYPSIN INHIBITOR PRECURSOR

Polymer:

1

Type:

protein

Length:

58

Chains:

A

Organism

Bos taurus

Amylase(ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE)

Classification:	Alpha Amylase
Structure Weight:	48016.77

Molecule:

ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE

Polymer:

1

Type:

protein

Length:

425

Chains:

A

EC#:

3.2.1.1

Mutation:

E208Q

Details:

COMPLEXED WITH MALTOPENTAOSE

Organism

Bacillus subtilis

Gene Names

amyE amyA BSU03040

 

 

 

Pepsin(X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUCTURE OF THE HEXAGONAL CRYSTAL FORM OF PORCINE PEPSIN AT 2.3 ANGSTROMS RESOLUTION)

Classification:	Hydrolase(acid Proteinase)
Structure Weight:	34469.80

Molecule:

PEPSIN

Polymer:

1

Type:

protein

Length:

326

Chains:

A

EC#:

3.4.23.1

Organism

Sus scrofa

Gene Name

PGA

Htra(Solution structure of HtrA PDZ domain from Streptococcus pneumoniae)

Classification:	Protein Binding
Structure Weight:	14890.90

Molecule:

Putative serine protease

Polymer:

1

Type:

protein

Length:

134

Chains:

A

Fragment:

PDZ domain, UNP residues 266-390

Organism

Streptococcus pneumoniae

Gene Name

SP_2239

Carboxypeptidase(CRYSTAL STRUCTURE OF BOVINE PANCREATIC CARBOXYPEPTIDASE A COMPLEXED WITH AMINOCARBONYLPHENYLALANINE AT 1.75 A)

Classification:	Carboxypeptidase
Structure Weight:	138865.59

Molecule:

CARBOXYPEPTIDASE A

Polymer:

1

Type:

protein

Length:

307

Chains:

A, B, D, E

EC#:

3.4.17.1

Organism

Bos taurus

Gene Names

CPA1 CPA