Macromolecular Structure

MACROMOLECULAR STRUCTURE
Biopolymers in Three Dimensions
(revised 08/17/2024)
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
Protein Structures 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	Pymol Scripts Trypsin Calpain COVID-19 Main Protease Phosphofructokinase Hexokinase Succinyl-CoA Synthetase Amidoribosyl Transferase Ribonuclease A
Motors	Images none	Pymol Scripts Actin Myosin V-ATPase
Viruses & Phages	Images none	Pymol Scripts QΒ VLP
Miscellaneous Protein Function	Images none	Pymol Scripts ATP synthase Beta propeller Capsid Qbeta Cellobiohydrolase Cellulose_synthase Cholera_adhesive Collagen Dynein Ferritin Gasdermin_d Light_harvesting Microtubule Phosphofructokinase Piezo2 Porin (big) Porin Respirasome Ribosome Silk Titin Transport Troponin_c v_ATPase Vault
Base, Nucleoside and Nucleotide Structures 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 Structures 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 Structures 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
Carbohydrate Structures Table of Contents
Carbohydrates	Images Glucose, etc	Pymol Scripts Mono & Disaccharides Amylopectin Amylose Carrageenan Cellulose Cellulose II (no pml file) Cellulose microfibrils (no pml file) Chitin_beta Covid spike glycosylated Curdlan (no pml file) Galactoglucan (no pml file) Glycogen Heparin Hyaluronic acid Keratan sulphate Protein glycan Starch Teichoic acid
Lipids, Amphipath and Membrane Structures 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