Glycolysis + TCA Cycle + ETC — 3D Reaction Mechanism Simulators

Each simulator is built from real crystal-structure coordinates (RCSB PDB), with mechanisms verified against primary literature (PubMed) and annotations from UniProt · PubChem · BRENDA.

★ Master Switch of Glycolysis — available now

REGULATOR

PFKFB3 (iPFK-2 / FBPase-2)

F6P + ATP → F2,6BP  |  F2,6BP + H₂O → F6P + Pᵢ

Bifunctional kinase + phosphatase that sets the level of F2,6BP, the most potent allosteric activator of PFK-1. Two active sites, two separate mechanisms.

EC 2.7.1.105 / EC 3.1.3.46 · PDB 2AXN·2DWP·2I1V·3QPW

▶ OPEN SIMULATOR

Why it matters: PFKFB3 controls glycolytic flux by making and breaking fructose-2,6-bisphosphate. Overexpressed in cancer cells (Warburg effect); a major drug target.

The 10 Glycolytic Steps

GLUCOSE
①
STEP 1

Hexokinase / Glucokinase

Glucose + ATP → G6P + ADP

Large induced-fit domain closure wraps around glucose; Mg²⁺-assisted in-line phosphoryl transfer, conserved Asp acts as catalytic base.

EC 2.7.1.1 · human HK1

▶ OPEN SIMULATOR
→
G6P
STEP 2

Phosphoglucose isomerase (PGI)

G6P ⇌ F6P

Aldose-ketose isomerization: ring opening, base-catalyzed proton abstraction via cis-enediol(ate) intermediate, ring closure.

EC 5.3.1.9

▶ OPEN SIMULATOR
→
F6P
STEP 3

Phosphofructokinase-1 (PFK-1)

F6P + ATP → F1,6BP + ADP

Rate-limiting committed step. Allosterically activated by AMP & F2,6BP, inhibited by ATP/citrate. In-line phosphoryl transfer onto the 1-OH.

EC 2.7.1.11

▶ OPEN SIMULATOR
→
F1,6BP
STEP 4

Aldolase (class I)

F1,6BP ⇌ DHAP + G3P

Retro-aldol cleavage through a Schiff-base (protonated imine) between Lys and C2 of the sugar; stabilized carbanion intermediate.

EC 4.1.2.13

▶ OPEN SIMULATOR
→→
DHAP + G3P
STEP 5

Triosephosphate isomerase (TPI)

DHAP ⇌ G3P

The perfect enzyme (kcat/KM at diffusion limit). Glu165 abstracts C1 proton through an enediolate intermediate, stabilized by a Lys-His pair ("catalytic loop").

EC 5.3.1.1

▶ OPEN SIMULATOR
STEP 6

GapDH dehydrogenase

G3P + Pᵢ + NAD⁺ → 1,3-BPG + NADH

Cys149 thiolate attacks the aldehyde → thiohemiacetal; hydride transfer to NAD⁺; phosphorolysis of the thioester → acyl phosphate.

EC 1.2.1.12

▶ OPEN SIMULATOR
→
1,3-BPG
STEP 7

Phosphoglycerate kinase (PGK)

1,3-BPG + ADP → 3PG + ATP

First ATP-producing step (substrate-level phosphorylation). Two domains hinge closed (~32°) around both substrates; arginine ladder stabilizes the TS.

EC 2.7.2.3

▶ OPEN SIMULATOR
→
3PG
STEP 8

Phosphoglycerate mutase (dimeric PGAM)

3PG ⇌ 2PG

Phosphohistidine (His11) shuttle: enzyme phosphorylates the substrate, then reclaims the phosphate at the adjacent position — a Ping-Pong swap.

EC 5.4.2.11

▶ OPEN SIMULATOR
→
2PG
STEP 9

Enolase

2PG ⇌ PEP + H₂O

Mg²⁺-dependent anti-elimination of water: Lys345 abstracts C2 proton while Glu211 donates OH leaving group → enolate (PEP).

EC 4.2.1.11

▶ OPEN SIMULATOR
↓
PEP
FERMENTATION · ANAEROBIC

Lactate Dehydrogenase (LDH)

Pyruvate + NADH → Lactate + NAD⁺  |  Lactate + NAD⁺ → Pyruvate + NADH

Names differ, directions differ. Anaerobic branch from pyruvate. LDHA (M-type) drives fermentation; LDHB (H-type) recycles lactate. Same mechanism, opposite kinetic preference — paralogous genes (chromosome 11 / 12).

EC 1.1.1.27 · human LDHA PDB 1I10 · LDHB PDB 1I0Z

▶ OPEN SIMULATOR FERMENTATION END · no continuation
←Lactate
↗pyruvate
STEP 10

Pyruvate kinase

PEP + ADP → Pyruvate + ATP

Allosteric homotetramer. PEP transfers its phosphate to ADP, and the resulting enol-pyruvate tautomerizes to pyruvate. K⁺/Mg²⁺ assisted.

EC 2.7.1.40

▶ OPEN SIMULATOR
→pyruvate
TCA GATE · AEROBIC

Pyruvate Dehydrogenase Complex (PDH)

Pyruvate + CoA + NAD⁺ → Acetyl-CoA + CO₂ + NADH + H⁺

Aerobic branch from pyruvate. Three enzymes — E1 (TPP decarboxylase), E2 (lipoyl transacetylase), E3 (dihydrolipoamide dehydrogenase) — ferry an acetyl group along a lipoyl "swinging arm" into the TCA cycle. Irreversible gate; regulated by PDK/PDP.

EC 1.2.4.1 · 2.3.1.12 · 1.8.1.4 · human E1 PDB 1NI4

▶ OPEN SIMULATOR AEROBIC · continues
→Acetyl-CoA
⤷ PYRUVATE branches → PDH → Acetyl-CoA → TCA cycle (aerobic)  |  LDH → Lactate (fermentation · Cori cycle)

The TCA (Krebs / Citric Acid) Cycle — 8 enzymes, all available

ACETYL-CoA
ⓐ
TCA 1

Citrate synthase (CS)

Acetyl-CoA + OAA → Citrate + CoA-SH

Irreversible gate of the cycle. His274 enolizes acetyl-CoA; Claisen condensation onto OAA, then thioester hydrolysis. Inhibited by ATP / NADH.

EC 2.3.3.1 · PDB 5CTS

▶ OPEN SIMULATOR
→
CITRATE
TCA 2

Aconitase (ACO)

Citrate ⇌ Isocitrate (via cis-aconitate)

[4Fe-4S] cluster coordinates the substrate. His101/FE4: dehydration to cis-aconitate then stereo-specific rehydration → isocitrate.

EC 4.2.1.3 · PDB 1ACO

▶ OPEN SIMULATOR
→
ISOCITRATE
TCA 3

Isocitrate dehydrogenase (NAD⁺ IDH3)

Isocitrate + NAD⁺ → α-KG + CO₂ + NADH

First oxidative decarboxylation. Hydride to NAD⁺ → oxalosuccinate, then metal-assisted decarboxylation to α-KG + CO₂.

EC 1.1.1.41 · PDB 6KDY

▶ OPEN SIMULATOR
→
α-KG + CO₂
TCA 4

α-Ketoglutarate DH complex (OGDH)

α-KG + CoA + NAD⁺ → Succinyl-CoA + CO₂ + NADH

PDH-like E1/E2/E3 machine. TPP decarboxylates α-KG; the lipoyl swinging arm carries the succinyl group; E3 makes NADH. Second CO₂ + NADH.

EC 1.2.4.2 · 2.3.1.61 · 1.8.1.4 · PDB 8I0K

▶ OPEN SIMULATOR
→
SUCCINYL-CoA
TCA 5

Succinyl-CoA synthetase (SCS)

Succinyl-CoA + GDP + Pi → Succinate + GTP + CoA-SH

Substrate-level phosphorylation. Catalytic His299 cycles His ⇄ phospho-His; thioester energy drives GTP synthesis from GDP + Pi.

EC 6.2.1.4 · PDB 2FP4

▶ OPEN SIMULATOR
→
SUCCINATE
TCA 6

Succinate dehydrogenase (SDH · Complex II)

Succinate + FAD → Fumarate + FADH₂

Membrane-bound, FAD-linked. His365 abstracts a proton; hydride to N5. FADH₂ feeds electrons via Fe-S clusters to ubiquinone (ETC).

EC 1.3.5.1 · PDB 1ZOY

▶ OPEN SIMULATOR
→
FUMARATE
TCA 7

Fumarase (fumarate hydratase · FH)

Fumarate + H₂O → L-Malate

Stereospecific anti-addition of water. RTHTQ loop: His235 is the general acid/base. Fully reversible lyase reaction.

EC 4.2.1.2 · PDB 5UPP

▶ OPEN SIMULATOR
→
L-MALATE
TCA 8

Malate dehydrogenase (MDH2)

L-Malate + NAD⁺ → OAA + NADH + H⁺

Cycle-closing oxidation. His182 abstracts the 2-OH proton; hydride to nicotinamide C4. The OAA regenerated starts the next turn.

EC 1.1.1.37 · PDB 2DFD

▶ OPEN SIMULATOR
ⓐ
OAA → CYCLES BACK
⤷ Per acetyl-CoA turn: 2 CO₂ · 3 NADH · 1 FADH₂ · 1 GTP → ≈10 ATP equivalent via the ETC. NADH/FADH₂ feed oxidative phosphorylation → Electron Transport Chain.

Oxidative Phosphorylation — the Electron Transport Chain (Complex I–V)

OXPHOS · NEW

Electron Transport Chain (Complex I · III · IV · V)

NADH + O₂ + ADP + Pᵢ → NAD⁺ + H₂O + ATP

Four mitochondrial complexes pass electrons from NADH (and FADH₂) to O₂ while pumping H⁺ across the inner membrane. Complex I oxidizes NADH (FMN + 8 Fe-S clusters); Complex III runs the Q-cycle; Complex IV reduces O₂ at the heme a₃–Cu_B binuclear center; Complex V (ATP synthase) turns the proton gradient into ATP.

PDB 4HEA · 1BGY · 1OCC · 1BMF

▶ OPEN SIMULATOR
⤷ Per NADH ≈ 2.5 ATP · per FADH₂ ≈ 1.5 ATP (chemiosmotic theory, Mitchell 1961).

How these simulators are built

  1. Mechanism research — primary literature via PubMed (kinetic isotope effects, trapped intermediates, transition-state analogs, mutagenesis).
  2. Structural data — real coordinates from RCSB PDB: apo, Michaelis complex, intermediate and transition-state-analog states are superposed into one frame.
  3. Ligand geometry — substrates/products from PubChem/PDB chemical component dictionaries.
  4. Animation — interpolation between real crystallographic states; electron-flow arrows, forming/breaking bonds, residue labels, per-step narration.

Every simulator includes a reference panel linking the exact PDB entries and PMID numbers used.