Caspase-3 - 3D Mechanism Simulator

Loading structural data… (1CP3)

References & Databases

START HERE — how to read Asp-Xaa cut on caspase-3 A single executioner-cut cartoon on the cleaved human caspase-3 / apopain frame that exists: 1CP3 (2.30 Å), chain A, with Ac-DVAD-fmk in the pocket. That motif is a named covalent occupancy, not DEVD and not the cut product. TITLE writes ACE-DVAD-FMC; SEQRES is ACE-Asp-Val-Ala-Asp-CF0 — coordinates match DVAD. CF0 C1 is occupied and is extracted (covalent adduct). The DEVD peptide is [schematic]. N-fragment, C-fragment, thioester, and water are [schematic]. Cys163 is UniProt Cys163. His121 is present. Gold H⁺ leaves water; blue is the Cys-SG nucleophile, not a hydride. Overlay peptide distances are not geomClaims. Dimer partner B is named occupancy, not animated. Executioner, not initiator. Caspase-7/8/9 are other genes. Not a pure A-page (E~acyl covalent).
Crystal structures PDB 1CP3 — human caspase-3 / apopain + Ac-DVAD-fmk, 2.30 Å (Mittl 1997). Coordinates are public. 1PAU is a companion soak — not this mesh. Caspase-7/8/9 structures are other genes. Caspase-7 is not a clone of this page.
Mechanism — Cys163 nucleophile, thioester, water hydrolysis Mittl et al., J. Biol. Chem. 1997, PMID:9045680 — recombinant human CPP32 with acetyl-Asp-Val-Ala-Asp fluoromethyl ketone. UniProt P42574 nucleophile is Cys163. His121 is the compiled general base and is present on this map. Product teaching = cleaved Asp-Xaa peptide (DEVD analog). Physiological substrates include PARP-1 and other executioner targets — analog, not this mesh. Source: Mittl 1997 · UniProt P42574
0 — Setup: Ac-DVAD-fmk occupies the scissile cleft 1CP3 holds cleaved caspase-3 and Ac-DVAD-fmk. That motif is the crystal occupant — not DEVD and not the cut product. Opaque, no autoplay. Chemistry below uses schematic DEVD peptide.Source: PDB 1CP3
① — DEVD analog presented A short DEVD analog docks as a named stand-in for an Asp-Xaa cut — [schematic], not DEVD crystal and not the fmk. Carbonyl faces Cys163. Overlay peptide Å are not geomClaims.Source: compiled caspase-3 substrate identity · UniProt P42574
② — Cys163 attacks C → covalent E~acyl (hypothetical, lit.-based) Blue nucleophile rides from Cys163 SG 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–S covalent distance (thioester — 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.Source: compiled caspase Cys · UniProt P42574
③ — C-fragment leaves (hypothetical, lit.-based) Schematic C-fragment departs. E~acyl stays on Cys163. Cut teaching = Asp-Xaa opened at one site.Source: EC 3.4.22.56 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 SG (thiol). 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. Thioester is hydrolysed — water-O mass is kept, not deleted. Overlay hydrolysis Å are not geomClaims.Source: compiled cysteine-protease hydrolysis · UniProt P42574
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. Caspase-7 is another gene, not a clone of this page. The fmk was occupancy, not this chemistry. Caspase-9 is the initiator, another gene.Source: EC 3.4.22.56 net accounting

How to read this page — a first-pass primer First pass: Setup (Ac-DVAD-fmk seated, Cys163 ★) → ① DEVD analog docks → ② blue SG → 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: 3.18 / 1.80 / 2.77 / 2.94 Å are crystal facts on occupied 1CP3 atoms; peptide, fragments, water, and H spheres are [schematic]. Third pass: open “Disagreements” for fmk ≠ DEVD, TITLE vs SEQRES, executioner vs initiator, and caspase-7 as another gene.
Chemistry primer — cysteine protease, executioner not initiator Caspase-3 cuts after Asp via a cysteinyl thioester, then water hydrolyses E~acyl. Gold = H⁺. Blue = Cys-SG nucleophile (not hydride). Teaching substrate = DEVD analog. This is not caspase-9 (initiator, other gene), and not caspase-7 (other gene, not a clone).
Words used on screen — occupancy · analog · executioner · fmk Occupancy — Ac-DVAD-fmk is the crystal ligand; never relabeled as DEVD. Analog — the peptide is a short model occupancy for an Asp-Xaa cut. Executioner — caspase-3 is downstream of caspase-9/8; this page is not the initiator. fmk — fluoromethylketone covalent adduct (CF0 C1 occupied on 1CP3).

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1CP3 (2.30 Å) with occupied Ac-DVAD-fmk atoms; Cys163 SG ⋯ INH DN = 3.18 Å; Cys163 SG ⋯ INH C1 = 1.80 Å; Arg64 NH2 ⋯ INH DOD2 = 2.77 Å; Arg207 NH2 ⋯ INH DOD1 = 2.94 Å. The inferred layer ([schematic]): DEVD 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. CF0 C1 is occupied (unlike 1JXQ) and is a measured covalent-adduct claim.
Disagreements on record (a) Ac-DVAD-fmk ≠ DEVD ≠ cut product. Occupancy. (b) TITLE writes ACE-DVAD-FMC; SEQRES is ACE-Asp-Val-Ala-Asp-CF0. Coordinates match DVAD. (c) Peptide ≠ physiological caspase-3 substrate. DEVD analog is a model occupancy. (d) Cys163 = UniProt Cys163. Screen uses PDB-author numbers that match UniProt here. (e) Capture vs hydrolysis split. Compiled cysteine protease writes two chemical events; this page plays five beats. (f) Executioner, not initiator. Caspase-9 is another gene. (g) Caspase-7 is another gene, not a clone of this page. (h) No protein-domain swing. (i) Not a pure A-page — E~acyl is covalent. (j) 1PAU is not this mesh. (k) CF0 C1 occupied — covalent adduct, named occupancy, not the teaching peptide.
Regulation — dimer · executioner · XIAP Dimerization of the p17/p12 heterodimer is the active form on 1CP3 — the dimer partner B is named occupancy, not a morph. Activation is by initiator caspases (caspase-9/8), named, not animated. XIAP is a compiled inhibitor, not this mesh.Source: UniProt P42574 · Mittl 1997 PMID:9045680
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 3.4.22.56 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 3.4.22.56 — no k_cat/K_m re-asserted
Sequence Human CASP3 UniProt P42574 · NCBI Gene 836. Screen uses 1CP3 numbering. Cys163 = UniProt Cys163. His121 = UniProt His121.
Simulation map — what you see is what is written Setup = 1CP3 Ac-DVAD-fmk seated (opaque, no autoplay). ① DEVD analog moves in (schematic). ② slow-mo: blue nucleophile SG → 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 1CP3: human caspase-3 / apopain + Ac-DVAD-fmk, 2.30 Å — public coordinates; measured occupied SG⋯DN = 3.18 Å · SG⋯C1 = 1.80 Å · Arg64 NH2⋯DOD2 = 2.77 Å · Arg207 NH2⋯DOD1 = 2.94 Å S2 — Mittl et al., J. Biol. Chem. 1997, PMID:9045680 — recombinant CPP32 with Ac-DVAD-fmk S3 — Sequence: UniProt P42574 (human CASP3) · NCBI Gene 836 S4 — Kinetics: BRENDA EC 3.4.22.56 — 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., DEVD peptide, N/C fragments, thioester, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

caspase-3dimer partnerONH⁺ (gold)nucleophile (blue)