Blue: moving part of the active site. Grey: its starting shape.
Teaching animation · real enzyme structuresLoading the measured enzyme and carbohydrate coordinates. The first visit needs an internet connection.
The unbound enzyme’s non-hydrogen atom positions are from 1HNY: wild-type human pancreatic α-amylase, X-ray resolution 1.80 Å. The 496-residue protein is not an AlphaFold prediction.
Glucose-unit coordinates come from 5TD4, an experimental amylase–carbohydrate structure. The two protein backbones are least-squares aligned.
Approach, separation, timing and the highlighted reaction are authored animation. There is no force-field, docking, energy or kinetic calculation.
The surface is a smoothed atomic envelope; the backbone is a Cα trace. Colours, bond thickness and the water’s added hydrogen positions are visual conventions, not photographs.
Important: 5TD4 contains the D300N mutant. We use it for carbohydrate geometry, not as the active enzyme. The displayed enzyme is the separate, unmutated 1HNY structure. This composite is not a single experimentally observed reacting complex.
The A-level extension compares the unbound 1HNY enzyme with the wild-type, acarbose-derived inhibitor-bound 1CPU enzyme (2.00 Å resolution). These are separate crystal structures, not consecutive frames from one experiment. A rigid least-squares fit uses matching Cα atoms excluding residues 303–312. Only like-for-like protein atoms are paired by chain, residue number, residue identity and atom name.
The bound structure loads when A-level is selected. Alignment statistics and the measured loop displacement will appear here.
Atom centres and Cα positions: unbound and bound endpoints come from the coordinate files. The blue trace highlights residues 303–312; this is a visual emphasis, not a claim that every other residue is immobile. Grey shows the same loop in 1HNY. Arrows show endpoint displacements, not forces, rates or bond stretching. All displacements are shown at 1×; there is no exaggerated-motion mode.
Between endpoints: Cartesian interpolation is a teaching device. Intermediate bond lengths and steric contacts are not validated, and the morph is not a physically resolved pathway. The surface is a smoothly deformed visual envelope, not a newly calculated solvent-excluded surface. Use atoms or backbone to inspect coordinates.
Starch reaction: the same conformational transition is coupled to the existing illustrative carbohydrate reaction. That composite is not an observed starch–enzyme complex. The apparent return during product release is also authored. In Crystal comparison, the actual inhibitor coordinates from 1CPU are shown instead and there is no hydrolysis.
What it establishes: the active-site region can adopt different conformations. These two static structures alone do not establish that binding happened before the conformational change, distinguish induced fit from conformational selection, or predict catalytic rates. The induced-fit sequence taught at A-level is a conceptual interpretation, not a deduction from these two snapshots alone.
The default 36-unit chain (or optional 60-unit chain) represents an unbranched, amylose-like starch chain at the same atomic scale as the enzyme. It is a teaching-sized model, not a claim that natural amylose has only this many units. Natural starch is a mixture of amylose and amylopectin; this viewer does not show branching or a starch granule.
Only the original short central chain comes directly from the 5TD4 coordinates, after the existing alignment and placement. The additional glucose rings are rigid copies of the measured ring geometry, linked through C1–O4 bonds and arranged using glycosidic single-bond rotations with an approximate steric screen. The extra units and their overall conformation are modelled, not experimentally observed. This is not a docking or force-field calculation, and it is not a validated equilibrium amylose helix. It preserves the original cleavage site and does not scale up the enzyme or glucose rings.
One highlighted bond is hydrolysed per cycle. When a long chain splits, each displayed product is correctly labelled as a shorter glucose chain, not as maltose unless it actually contains two glucose units. Repeated digestion, branching, granular starch and product distributions are not simulated.
The chain geometry and source-versus-modelled unit counts are reported here after loading.
One molecule of water is used in the net hydrolysis. Its O and two H atoms are tracked into the products; other substrate hydrogens are omitted. The transient glycosyl–enzyme intermediate and proton-transfer sequence are not animated. No actual reaction time or rate is implied.
This is not a model of a whole starch granule. Starch contains amylose and branched amylopectin. Human α-amylase hydrolyses internal α(1→4) linkages, not the α(1→6) branch links. Products include maltose, maltotriose and dextrins; other enzymes complete digestion to glucose.
Open in a desktop browser. No account, installation or student data is required. The online edition retrieves Three.js and two public PDB files, then constructs the optional longer chain locally. A-level additionally loads 1CPU for the conformational comparison. After all three structures load, “Save offline copy” makes a self-contained HTML file containing the library and structural data. A GPU-enabled browser is still required.
Protein Data Bank coordinate data: CC0. Three.js r152.2: MIT license, © 2010–2023 Three.js authors. Source references retrieved 9 September 2026. This application does not collect analytics.
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