Experimental protein coordinates can be loaded from the Protein Data Bank. The transport paths and shape changes are teaching animations—not measured atomic trajectories.
5VK6Potassium channel
KcsA, a bacterial channel. Four channel subunits are reconstructed from the deposited biological-assembly transforms; antibodies are omitted. This engineered structure captures an open, conducting channel.
RCSB structure ↗4ZW9Glucose carrier
Human GLUT3 with bound glucose. The measured structure is outward-occluded. The full alternating-access motion here is a schematic deformation, not an experimentally measured series of conformations.
RCSB structure ↗7E21Sodium–potassium pump
Human Na⁺/K⁺-ATPase in an inward-accessible state, prepared with an ATP analogue. Three Na⁺ out, two K⁺ in, one ATP per cycle. The animation simplifies the intervening states.
RCSB structure ↗ATP → ADP + PᵢATP chemistry
ATP uses the wwPDB Chemical Component Dictionary atom names, bonds and ideal heavy-atom coordinates. ADP retains the same atoms except for the terminal PO₃ group. Water supplies the fourth oxygen of released inorganic phosphate. ATP data are embedded and work offline.
When the experimental pump and its ATPγS ligand are available, a modelled ATP pose uses the analogue’s corresponding atom positions, replacing its terminal sulfur with oxygen at a modelled P–O distance. The attachment oxygen comes from Asp376. If those coordinates are unavailable, a clearly labelled illustrative scaffold and pocket placement are used.
ATP atom and bond data ↗ · ATP ↗ · ADP ↗
What has been simplified?
The bilayer uses modelled head-and-two-tail phospholipids, not an experimental membrane. Most water, hydrogen atoms, lipids, membrane proteins and other cell contents are omitted. Oxygen and glucose retain molecular geometry; tracking halos, colours and arrows are visual aids.
Protein colours aid recognition. “Clarity” deliberately uses a generated scaffold. “Molecular” uses experimental coordinates only when successfully loaded; otherwise the status strip explicitly identifies the scaffold. “Inspect measured structure” freezes the original protein coordinates and hides the teaching transport animation.
Membrane orientation uses OPM coordinates where available, otherwise a geometry-based alignment of the transmembrane helices. Carrier and pump motions are simplified deformations of one structure; they do not preserve every bond length. Do not use them to infer atom-by-atom mechanisms.
Particles move in both directions during passive transport. Relative concentrations are held fixed to compare net movement; this is not a closed system equilibrating over time. For the channel example the voltage difference is treated as zero. In cells, ions follow their electrochemical gradient.
The ATP close-up is magnified; molecules in the main view use the same coordinate scale as the protein. The pump attachment residue is highlighted; the faint contextual trace in the inset is decorative, not an additional measured protein segment. The sequence shows phosphate transfer to the pump, ADP release, and later hydrolysis of the phosphoenzyme. It is not a calculated reaction trajectory. Most hydrogens, proton transfers, Mg²⁺ coordination and changing protonation states are omitted. The overall ATP + H₂O → ADP + Pᵢ reaction drives the cycle; breaking a bond alone does not release energy.
The Na⁺/K⁺ pump is one example of active transport, not the mechanism of every active transporter. Switching ATP off resets the illustration to an unpowered starting state. Osmosis, cotransport and bulk transport are outside this first version.
No installation, login or analytics. File imports remain in this browser. Space: play/pause. ← / →: step. 1–4: switch mechanism.