Retrieving Structural Data of a Protein Using PDB Database

Knowing the 3D structure of a biological macromolecule is essential for understanding

1. its role in human and animal health and disease

2. its function in plants, food and energy production

3. its importance to other topics related to global sustainability

Proteins

are the fundamental units of all living cells. they preform a large variety of biological tasks.

protein structure depend on

based on the chemical and physical properties of the amino acids of the peptide sequence.

Amino Acids types

1. Non-polar

2. +ve charge

3. Polar

4. -ve charge

Levels of protein structure

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Primary Structure

The simplest level of protein structure is simply the sequence of amino acids in a polypeptide chain . It is synthesized during transcription.

Secondary Structure

local folded structures that forms within a polypeptide due to interactions between atoms of the backbone

what does the backbone refer to

The polypeptide chain without the R groups

The most common secondary structure are the

1. Alpha helix

2. Beta pleated sheets

structure in secondary protein are held by

hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another

Tertiary structure

the overall 3D structure

Quaternary structure

made up if multiple polypeptide chains, also known as subunits.

PDB stands for

Protein Data Bank

The Protein Data Bank is

a database for the Three-dimensional structure data of large biological molecules, such as proteins and nucleic acids

The data found in PDB are

1. X-ray Crystallography

2. NMR spectroscopy

3. Cryo-electron microscopy

Member organisations

PDBe, PDBj, RCSB, BMRB

Worldwide Protein Data Bank (wwPDB)

The PDB is overseen by an organization

RCSB stands for

Research Collaboratory for Structural Bioinformatics

File format

FASTA

first format used by PDB was called

PDB file format

In 1996 which format was introduced

mmCIF

mmCIF stands for

macromolecular Crystallographic Information file

PDB ID

the 4-character unique identifier of ever entry in the PDB

Classification

refers to the classification type pf the protein

Organism(s)

Refers to the organism of origin for the protein

Expression System

the organism used to express this protein

Mutation

Indicate whether or not this structure entry contains mutations

Experimental Data Snapshot

Lists the experimental methods used for de