Free Interactive Activity
Enzyme Active Site Lab
Watch the full chemical structure of a serine-protease active site and its substrate. Drag the peptide in, then change pH, temperature, or salt — and see protons hop, charges appear, and the catalytic bonds form and break.
Asp102
COO⁻
His57
HIm
Triad
Active
Substrate
Free
Relative catalytic activity
Controls
Heat makes every atom vibrate harder; past ~70°C the geometry breaks and the enzyme denatures.
Low pH protonates Asp (COO⁻ → COOH, triad breaks). High pH leaves His unable to donate a proton.
Salt screens the Asp–His charge interaction, weakening the catalytic relay.
Drag the peptide (top-right) into the pocket to dock it.
Learning objectives
- Read the structural formula of the catalytic triad and the peptide substrate.
- Connect pH to protonation: which H atoms appear or vanish on Asp and His.
- Trace the proton relay Asp → His → Ser and the nucleophilic attack that forms the tetrahedral intermediate.
Chemical formulas
- Asp102 side chain: –CH₂–COO⁻ ⇌ –CH₂–COOH
- His57 side chain: imidazole ring (C₃H₃N₂), HIm ⇌ HImH⁺
- Ser195 side chain: –CH₂–O–H (the nucleophile Oγ)
- Substrate: peptide –NH–CHR–C(=O)–NH– (scissile bond)
- Oxyanion hole: two backbone N–H donors stabilizing C–O⁻
Try this
- At pH 7.5, drag the peptide in — watch Ser's H jump to His and the green C–O bond form.
- Drop pH to 2: an H appears on Asp (COOH) and on His — the relay breaks, catalysis stops.
- Raise ionic strength to 90 — the Asp–His bond fades even at ideal pH.
- Heat to 85°C and watch the whole structure shake apart.
This is a coarse-grained structural model of a serine-protease active site, not a full QM/MM simulation. Want AI-built lessons, quizzes, and chatbots around it?