Protein Data Bank(PDB)

Assalamualaikum,

Welcome everybody,today we would like to explain about Protein Data Bank.

The Protein Bank (PDB) is a repository for the three-dimensional structural data for 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.

X-Ray Crystallography

• A target is selected for structure determination
• The material is purified and then crystallized
• Crystals are put in front of an X-ray beam and diffracted intensities are collected on a detector
• These data are then analyzed using different computational methods

Data Deposition

PDB Extract Tool

• pdb_extract can extract information from the output of standard crystallographic programs.
• It merges the information into mmCIF files at each step of the structure-determination process.
• These mmCIF are then ready for validation and deposition.

AutoDep Input Tool

• ADIT is used for assembling, editing, validating and deposition structural data.
• It is built on top of the mmCIF dictionary.

PDB Validation Suite

• Creates reports based upon the validation results.
• Also calculates derived information that could be used for assessing the quality of a structure.

For more information on process of data deposition,click here.

Examples of protein structure images with their description:

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
Organism	Bacillus subtilis

THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS

Classification	Complex (proteinase/inhibitor))
Structure weight	29892.08
Molecule	BETA-TRYPSIN
Polymer	1
Type	Protein
Length	223
Chains	E
Organism	Bos taurus

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
Organism	Sus scrofa

SOLUTION STRUCTURE OF HTRA PDZ DOMAIN FROM STREPTOCOCCUS PNEUMONIA

Classification	Protein Binding
Structure weight	14890.90
Molecule	Putative serine protease
Polymer	1
Type	Protein
Length	134
Chains	A
Organism	Streptococcus pneumoniae

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
Organism	Bos taurus

SMILES

Assalamu'alaikum.

Welcome to the geniuses lair, everybody. Today we are going to learn about SMILES.

SMILES is Simplified Molecular-Input Line-Entry System. This program is used to translate a chemical three-dimensional structure into a string of symbols that is easily understood by a computer software.
SMILES is a easily-learned and flexible notation. The SMILES notation requires us to learn a handful of rules.

For example, this Morphine structure. I will demonstrate the function of this program by using this example.



By using SMILES you can translate the above structure which is Morphine CAS RN 57-27-2, into linear representation of the molecule so that a computer program can understand the structure.

Here is one SMILES Notation for CAS RN 57-27-2
Oc1ccc2CC(N3C)C$C=CC(o)C5Oc1c2C45CC3

Before I forget, this is how we represent atoms in their corresponding SMILES notations.

Atoms	SMILES notation
methane (CH4)	C
water (H2O)	O
hydrogen sulfide (H2S)	S
ammonia (NH3)	N
phosphine (PH3)	P
hydrogen chloride (HCl)	Cl

And this is how a bond is represented in SMILES notation.

Bonds	SMILES notation
single	-
double	=
triple	#
aromatic	:

To master this SMILES notation, u can learn further by clicking here.