Granzyme B - 3D Mechanism Simulator

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References & Databases

START HERE — how to read Asp-Xaa cut on granzyme B A single killer-cell serine-protease-cut cartoon on the human granzyme B frame that exists: 1IAU (2.00 Å), chain A, with Ac-IEPD-CHO in the pocket. That motif is a named aldehyde occupancy, not IEPD substrate and not the cut product. TITLE writes AC-IEPD-CHO; SEQRES is ACE-Ile-Glu-Pro-ASJ — coordinates match IEPD-CHO. ASJ C is occupied and is extracted (hemiacetal adduct). Dual occupancy on Ser195+ASJ: majority alt B (0.62) is this mesh; alt A (0.38) is not. The IEPD peptide is [schematic]. N-fragment, C-fragment, ester, and water are [schematic]. Ser195 is UniProt Ser203 (chymotrypsinogen numbering on this deposit). His57 is UniProt His64. Asp102 is UniProt Asp108. Gold H⁺ leaves water; blue is the Ser-OG nucleophile, not a hydride. Overlay peptide distances are not geomClaims. This is a serine protease, not a caspase. Perforin is Overview, not motion. Granzyme A/K/H/M are other genes. Caspases are other genes. NAG / Zn / glycan are not this mesh. Not a pure A-page (E~acyl covalent).
Crystal structures PDB 1IAU — human granzyme B + Ac-IEPD-CHO, 2.00 Å (Rotonda 2001). Coordinates are public. NAG glycans and Zn ions are crystallization occupancy — not this mesh. 1FQ3 (uninhibited) and 1FI8 (rat + ecotin) are companions, not this page. Granzyme A/K/H/M structures are other genes. Caspase crystals are other genes.
Mechanism — Ser195 nucleophile, ester, water hydrolysis Rotonda et al., Chem. Biol. 2001, PMID:11325591 — human granzyme B with acetyl-Ile-Glu-Pro-Asp-aldehyde. UniProt P10144 nucleophile is Ser203; screen Ser195 is that residue in chymotrypsinogen numbering. His57 / Asp102 are the compiled triad and are present on this map. Product teaching = cleaved Asp-Xaa peptide (IEPD analog). Physiological substrates include caspase-3 and Bid — analog, not this mesh. Source: Rotonda 2001 · UniProt P10144
0 — Setup: Ac-IEPD-CHO occupies the scissile cleft 1IAU holds granzyme B and Ac-IEPD-CHO. That motif is the crystal occupant — not IEPD substrate and not the cut product. Opaque, no autoplay. Chemistry below uses schematic IEPD peptide.Source: PDB 1IAU
① — IEPD analog presented A short IEPD analog docks as a named stand-in for an Asp-Xaa cut — [schematic], not IEPD crystal and not the aldehyde. Carbonyl faces Ser195. Overlay peptide Å are not geomClaims.Source: compiled granzyme B substrate identity · UniProt P10144
② — Ser195 attacks C → covalent E~acyl (hypothetical, lit.-based) Blue nucleophile rides from Ser195 OG to analog C. Intact peptide fades in place to schematic N-fragment + C-fragment; the carbonyl C then slides to a real ~1.8 Å C–O covalent distance (ester — the E~acyl bond length, no 3.2 Å gap). Overlay peptide Å are not geomClaims. Slow-motion on purpose. Not a pure A-page. Serine protease, not a caspase.Source: compiled serine-protease Ser · UniProt P10144
③ — C-fragment leaves (hypothetical, lit.-based) Schematic C-fragment departs. E~acyl stays on Ser195. Cut teaching = Asp-Xaa opened at one site.Source: EC 3.4.21.79 net accounting
④ — Water hydrolyses E~acyl (hypothetical, lit.-based) A schematic water moves in (glides) to the E~acyl face. Gold H⁺ leaves water H2 on the yellow arrow and vanishes right at the arrow tip at the leaving OG (Ser195). Remaining O–H = OH⁻ attacks the carbonyl along the blue arrow; after the swap the water O is bound as the new carboxylate O on the N-fragment (red ball) and leaves with it. Ester is hydrolysed — water-O mass is kept, not deleted. Overlay hydrolysis Å are not geomClaims.Source: compiled serine-protease hydrolysis · UniProt P10144
⑤ — N-fragment leaves — cut [schematic] N-fragment departs carrying its new carboxylate O (from H₂O) — the red water O rides out bound to the product. Product teaching = cleaved Asp-Xaa peptide. This is not a caspase. Perforin is Overview, not motion. The aldehyde was occupancy, not this chemistry. Granzyme A/K/H/M are other genes.Source: EC 3.4.21.79 net accounting

How to read this page — a first-pass primer First pass: Setup (Ac-IEPD-CHO seated, Ser195 ★) → ① IEPD analog docks → ② blue OG → C, peptide becomes N + C fragments → ③ C-fragment leaves → ④ gold H⁺ then OH⁻ attacks E~acyl → ⑤ N-fragment leaves; cut. Second pass: 2.73 / 1.48 / 2.87 / 3.74 Å are crystal facts on occupied 1IAU alt-B atoms; peptide, fragments, water, and H spheres are [schematic]. Third pass: open “Disagreements” for CHO ≠ IEPD substrate, chymotrypsinogen vs UniProt numbering, serine vs caspase, dual occupancy, and perforin not motion.
Chemistry primer — serine protease, not a caspase Granzyme B cuts after Asp via a seryl ester, then water hydrolyses E~acyl. Gold = H⁺. Blue = Ser-OG nucleophile (not hydride). Teaching substrate = IEPD analog. This is not caspase-3 / 8 / 9 (cysteine proteases, other genes), and not a perforin-pore movie.
Words used on screen — occupancy · analog · CHO · triad numbering Occupancy — Ac-IEPD-CHO is the crystal ligand; never relabeled as IEPD substrate. Analog — the peptide is a short model occupancy for an Asp-Xaa cut. CHO — aldehyde hemiacetal adduct (ASJ C occupied on 1IAU, majority alt B). Ser195 / His57 / Asp102 — chymotrypsinogen numbering on this deposit = UniProt Ser203 / His64 / Asp108. Perforin — Overview, not motion.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1IAU (2.00 Å) with occupied Ac-IEPD-CHO atoms (majority alt B, 0.62); Ser195 OG ⋯ INH DN = 2.73 Å; Ser195 OG ⋯ INH DC = 1.48 Å; Arg226 NH2 ⋯ INH DOD2 = 2.87 Å; Gly193 N ⋯ INH DO = 3.74 Å. The inferred layer ([schematic]): IEPD peptide, N/C fragments, E~acyl, water, transferring H⁺/nucleophile spheres, product leave, and capture/hydrolysis split. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay peptide contacts are not geomClaims. ASJ C is occupied (hemiacetal) and is a measured covalent-adduct claim. His57 NE2 ⋯ Ser195 OG is ~5.00 Å on this adduct — present, not a close H-bond claim.
Disagreements on record (a) Ac-IEPD-CHO ≠ IEPD substrate ≠ cut product. Occupancy. (b) TITLE writes AC-IEPD-CHO; SEQRES is ACE-Ile-Glu-Pro-ASJ. Coordinates match IEPD-CHO. (c) Peptide ≠ physiological granzyme B substrate. IEPD analog is a model occupancy. (d) Ser195 = UniProt Ser203 (chymotrypsinogen numbering; REMARK 999). His57 = UniProt His64. Asp102 = UniProt Asp108. Plan 64/108/203 is UniProt, not PDB-author. (e) Dual occupancy Ser195+ASJ: majority alt B (0.62) extracted; alt A (0.38) not this mesh. (f) Capture vs hydrolysis split. Compiled serine protease writes two chemical events; this page plays five beats. (g) Serine protease, not a caspase. Caspase-3/8/9 are other genes. (h) Granzyme A/K/H/M other genes. (i) Perforin is Overview, not motion. (j) No protein-domain swing. (k) Not a pure A-page — E~acyl is covalent. (l) NAG / Zn are crystallization occupancy, not this mesh. (m) ASJ C occupied — hemiacetal adduct, named occupancy, not the teaching peptide. (n) His57⋯Ser195 OG ~5 Å on this aldehyde adduct — triad residues are present; a close catalytic H-bond is not claimed from these coordinates.
Regulation — zymogen · perforin · killer cell Activation is by cathepsin C (dipeptidyl peptidase I) of the zymogen — named, not animated. Delivery into the target cell is by perforin — Overview, not motion. Isozymes granzyme A/K/H/M are other genes.Source: UniProt P10144 · Rotonda 2001 PMID:11325591
Kinetics scope (no measured timecourse on this page) One Asp-Xaa cleavage event is drawn, not a steady-state run. Compiled BRENDA values for EC 3.4.21.79 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 3.4.21.79 — no k_cat/K_m re-asserted
Sequence Human GZMB UniProt P10144 · NCBI Gene 3002. Screen uses 1IAU chymotrypsinogen numbering. Ser195 = UniProt Ser203. His57 = UniProt His64. Asp102 = UniProt Asp108.
Simulation map — what you see is what is written Setup = 1IAU Ac-IEPD-CHO seated (opaque, no autoplay). ① IEPD analog moves in (schematic). ② slow-mo: blue nucleophile OG → C; peptide fades to N + C fragments. ③ C-fragment leaves. ④ gold H⁺ then OH⁻ attacks E~acyl. ⑤ N-fragment leaves; cut. Only these events move.
Sources — bibliography of this page S1 — PDB 1IAU: human granzyme B + Ac-IEPD-CHO, 2.00 Å — public coordinates; measured occupied OG⋯DN = 2.73 Å · OG⋯DC = 1.48 Å · Arg226 NH2⋯DOD2 = 2.87 Å · Gly193 N⋯DO = 3.74 Å (majority alt B) S2 — Rotonda et al., Chem. Biol. 2001, PMID:11325591 — human granzyme B with Ac-IEPD-CHO S3 — Sequence: UniProt P10144 (human GZMB) · NCBI Gene 3002 S4 — Kinetics: BRENDA EC 3.4.21.79 — no k_cat/K_m re-asserted on this page

› Backbones and ligand poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., IEPD peptide, N/C fragments, ester, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

granzyme BONH⁺ (gold)nucleophile (blue)