https://pdb101.rcsb.org/

Primary structure

Amino acids, forming a Polymer by Dehydration synthesis, forming a bond called a Peptide bond. A protein is thus called a polypeptide.

Proteins are Chiral molecules, because amino acids are. The peptide bonds can be in Cis or Trans conformation. Almost all bonds are Trans, due to steric hindrances.

Geometrical structure of peptide bonds. They are planar due to sp2 hybridization

Secondary structure

phi and psi angles are (approximately) the only degrees of freedom left, given constraints of chemical bond angles, sizes, and other steric hindrances.

Ramachandran plot, residue unit, peptide unit

Stabilized partially, by Hydrogen bond between a Carbonyl group, and a NH.

$\alpha$-helix.

$\beta$-sheets

$\beta$-barrel

loops, random coils

video

Tertiary structure

loops, turns, random coils

folds, domains.

Quaternary structure

vid

Experimental techniques

Protein purification

Protein structure analysis

Types of proteins

Enzymes

Protein folding – Protein structure prediction

Protein structure visualization

Pymol, Jmol, JSmol, GLmol, https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html, http://proteinformatics.charite.de/ngl/html/ngl.html

http://getlig.com/