Experimental structures show the endpoints. Animation explains the ideas; it is not a simulation of molecular forces or folding kinetics.
OCR A coverage
Biological molecules, 2.1.2(k–o): amino acid structure; peptide bonds and condensation / hydrolysis; primary, secondary, tertiary and quaternary structure; hydrogen bonding, ionic interactions, disulfide bonds and hydrophobic / hydrophilic interactions. Examples include haemoglobin, insulin, a named enzyme, collagen, keratin and elastin.
OCR Biology A specification ↗
Real coordinates, built into this file
1CRN — crambin ↗: experimental X-ray coordinates, 1.50 Å resolution, 46 residues and 327 non-hydrogen atoms. This small plant protein contains two helical regions, a short antiparallel sheet and three disulfide bonds. It is used to connect the levels of structure in one molecule, not as a named enzyme example.
The embedded coordinates preserve the deposited structure up to a rigid rotation, translation and rounding. A backbone tube is a trace through Cα atoms, not an extra physical structure.
Experimental assemblies — optional first download
4HHB · human deoxyhaemoglobinFour chains, α₂β₂; each carries a haem group. The snapshot has no bound oxygen.PDB entry ↗ 4INS · insulinChains A and B are selected to show one two-chain insulin molecule, not the whole crystal / storage assembly.PDB entry ↗ 1BKV · collagen-like triple helixA synthetic 30-residue collagen-like model peptide, not a full collagen fibril. Three chains form a triple helix; these are not three α helices.PDB entry ↗ Downloads are requested only when you select an assembly. A clearly labelled schematic preview is used until an experimental structure has loaded. No generated subunit geometry is labelled as experimental.
Includes crambin, the renderer, chemistry models and any assembly coordinates successfully loaded in this session. No account, installation or analytics.
Useful simplifications
Classroom views. Each chapter opens in Clear view. In the amino-acid chapter, a single interactive structural diagram switches from the general R-group formula to named examples; it is not a stereochemical projection and does not imply a planar molecule. Longer R groups use condensed notation. Select a group rather than playing an animation. The 3D option shows modelled geometry; in the general model, the gold R marker is a placeholder, not an atom.
Amino acids. Small-molecule coordinates are generated with RDKit, not measured crystal structures. Neutral backbone formulas are used to make condensation clear; free amino acids are mainly zwitterions at typical cellular pH. Lysine and glutamate side-chain charges are shown separately. Hydrogens are omitted from large experimental protein structures, except modelled donor hydrogens in the hydrogen-bond view.
Peptide-bond diagrams. The default is one animated displayed structural formula, not a Haworth projection. All 23 atoms of alanine + glycine are shown explicitly and use the same atom identities as the 3D model. Source-coloured rings trace the carboxyl OH and amino H into water; gold highlights the new C–N peptide bond. On narrow screens the formula is arranged vertically, without changing connectivity. Displayed bond lengths, angles and motion are illustrative, not stereochemical information.
Peptide bond. The animation conserves atoms and shows the net condensation / hydrolysis reaction. It does not claim that free amino acids spontaneously condense in water, or reproduce the ribosome’s activated-tRNA mechanism.
Folding. The extended pose and path are illustrative. Backbone dihedral angles are changed while retaining covalent bond lengths and angles; the final folded pose is experimental. Intermediate poses are not energy-minimised and can contain steric overlaps. Disulfide links are revealed at the folded endpoint, not assigned a measured order of formation. Secondary structures are local arrangements, not compulsory sequential stages.
Interactions. Dashed backbone hydrogen-bond candidates are inferred from the experimental geometry, with donor hydrogens modelled. The three disulfides are Cys3–Cys40, Cys4–Cys32 and Cys16–Cys26. Ionic and hydrophobic close-ups are general schematics, not measured individual contacts in crambin. Hydrophobic-core wording applies to typical soluble globular proteins, not every protein.
Quaternary structure. Separating and bringing together subunits is an exploded-view illustration. It does not add peptide bonds between subunits or represent an experimental assembly pathway. Insulin has two polypeptide chains linked by disulfides; introductory classifications differ, but the chain count and connectivity shown here are explicit.
Globular and fibrous examples
Lysozyme: a globular enzyme that hydrolyses bonds in bacterial cell-wall peptidoglycan. Insulin: a globular hormone involved in lowering blood glucose. Haemoglobin: a conjugated globular protein with haem prosthetic groups. Collagen: tensile strength. Keratin: protective structural material. Elastin: stretch and recoil. OCR A does not require detailed fibrous-protein structures in this part of the specification.
RCSB PDB-101 educational resources ↗ · wwPDB data usage (CC0) ↗