MACROMOLECULAR STRUCTURE
Biopolymers in Three Dimensions

(revised 11/20/2021)
Loren Dean Williams, Georgia Tech

This page and the information contained on it are intended to facilitate the incorporation of 3D structures and visualization into the teaching of biochemistry and biophysics. This page contains images and PyMol Command Files (i.e., PyMol Scripts) for a broad variety of macromolecules commonly used in teaching biochemistry. Others can copy, distribute, display, and make derivative works for non-commercial purposes, so long as attribution is given.

Table of Contents
Basic Thermodynamics
Molecular Interactions
Proteins
DNA
RNA
Carbohydrates
Membranes
Extras
Williams Home

Basic Thermodynamics
Enthalpy, entropy and free energy
Document
none
Molecular Interactions
Table of Contents
Molecular Interactions
English Document
Spanish Document
Ions
The hydrophobic effect
Small molecule library
Pymol Scripts
Short Range Repulsion
Water
GC Base Pair
Electrostatic Interactions
Proteins
Table of Contents
Amino Acids and Peptides
Images
United States of Amino Acids
Venn Diagram
Amino Acid Flash Cards
Amino acids
The peptide bond
Φ/Ψ torsion angles
Pymol Scripts
Peptide Bond
Φ/Ψ
Protein secondary structure
Images
Sheets and Helices
α-Helix
β-Sheet
Loops and turns
Pymol Scripts
α-Helix
Coiled-Coil
Parallel β-Sheet
Antiparallel β-Sheet
β-Turn
Protein Folds
Images
Fibrous proteins
α-Helical proteins
α-Helical/β-Sheet proteins
Anti-parallel β-sheet proteins
Parallel β-sheet proteins
Pymol Scripts

Protein Folds
Collagen
Albumin
Myoglobin
Hemoglobin
Seven Transmembrane α-Helices
Carboxypeptidase
Ribonuclease A
TIM Barrel
OB Fold
Porin
Peptide Amyloid
Full Length Amyloid
HMW1 Adhesin
Groel
Evolution of Folding
Intrinsically Disordered Proteins
Images
none
Pymol Scripts
Intrinsic Disorder
Interactions of Proteins with Metals
Images
Metals (radii, coordinate numbers, etc)
Potassium Channel
Pymol Scripts
Calmodulin
Nitrogenase
Interactions of Proteins with Nucleotides
Images
Rossman Fold
Pymol Scripts
none
Enzymes and Catalysis
Images
Serine Proteases

Trypsin
Calpain
COVID-19 Main Protease
Phosphofructokinase
Hexokinase
Succinyl-CoA Synthetase
Amidoribosyl Transferase
Motors
Images
none
Pymol Scripts
Actin
Myosin
V-ATPase
Viruses & Phages
Images
none
Pymol Scripts
QΒ VLP
Bases, Nucleosides and Nucleotides
Table of Contents
Bases, Nucleosides and Nucleotides
Images
ribose/deoxyribose
bases
base pairs, triplets and quartets
Pymol Scripts

ATP
Syn/Anti
Sugar Pucker
Hoogsteen Base Pair
DNA
Table of Contents
DNA Structure
Images and Tables
phosphodiester backbone
A,B,Z conformation
Supercoiling
Pymol Scripts

B-Form DNA
DNA Torsion Angles
DNA Quadruplex
DNA Triplex
Interactions of DNA with small molecules
Images
Water
Magnesium
Spermine
Minor groove binders
Intercalators and Bis-intercalators
Pymol Scripts
Spine of Hydration
Interactions of DNA with Proteins
Images
Nucleosome
Polymerases
β-ribbon
Restriction and Modification Enzymes
Pymol Scripts
HU Protein Pymol Script
DNA Ligase Pymol Script
Nucleosome Pymol Script
P22 Repressor: HTH Pymol Script
TBP Pymol Script
Bacillus DNA Polymerase I Pymol Script
Zinc Finger Pymol Script
Bam HI
Eco RI
Fok I
Not I Pymol Script
Pvu II Pymol Script
RNA
Table of Contents
RNA Structure
Images, etc
GNRA Tetraloops
Kink-Turns
tRNA
Ribosome
motifs
Pymol Scripts
A-Form RNA
GNRA Tetraloop
20 Superimposed GNRA Tetraloops
Loop-E Motif
Helix 26a
Kink-Turn
tRNA
RNase P
Small Ribosomal Subunit
Thermus Thermophilus Ribosome
Ribosomal Tunnel
Interactions of RNA with Proteins
Images
Polymerases
tRNA synthetases
Pymol Scripts

Toll-like Receptor
Ribosomal Proteins
Class I: Glutamyl-tRNA sythetase
CRIPSR Cas
ro-RNA
Yeast RNA Pol II
Carbohydrates
Table of Contents
Carbohydrates
Images
Glucose, etc
Pymol Scripts
Monosaccharides and Disaccharides
Cellulose
Amylose
Glycogen
Glycosylated Spike Protein
Lipids, Amphipaths and Membranes
Table of Contents
Lipids, Amphipaths and Membranes
Images
none
Pymol Scripts
Membrane
Cholesterol Binding Protein
Tools and Extras
Table of Contents
Databases

Databases
PDB, CSD, PubMed
How to use the PDB
Tools
DNA Builder
Coiled-Coil Builder
PyMol Cheat Sheets

Pymol Documentation
PyMol Template Script

Initial support provided by the NSF CAREER Program