8VP4: JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO

Crystal Structure of JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO. Determined by X-ray diffraction at 1.51 Å resolution. Released 9 Apr 2025.

Method: X-ray diffraction
Resolution: 1.51 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,058
Mol. weight: 64.47 kDa
Released: 9 Apr 2025

Explore 8VP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VP4 contains 17 α-helices and 40 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	358	1	1
β-strand	364-368	5	2
β-strand	374	1	3
α-helix	375-376	2
β-strand	377-379	3	4
β-strand	383-384	2	4
α-helix	385-397	13
α-helix	403-416	14
β-strand	430	1	5
β-strand	434-437	4	2
β-strand	442	1	6
α-helix	1188-1190	3
β-strand	1191	1	6
β-strand	1200-1206	7	2
α-helix	1222-1235	14
β-strand	1238-1244	7	2
α-helix	1248-1259	12
α-helix	1262-1266	5
β-strand	1269-1275	7	2
β-strand	1278-1279	2	7
β-strand	1282-1284	3	7
β-strand	1290-1292	3	7
α-helix	1293-1299	7
α-helix	1306-1308	3
β-strand	1313-1318	6	2
β-strand	1324	1	3
β-strand	1326	1	5
β-strand	1329-1330	2	8

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	357-358	2	8
β-strand	364-368	5	2
β-strand	374	1	9
α-helix	375-376	2
β-strand	377-379	3	10
β-strand	383-384	2	10
α-helix	385-397	13
α-helix	403-416	14
β-strand	430	1	11
β-strand	434-437	4	2
β-strand	442	1	12
β-strand	1191	1	12
β-strand	1200-1206	7	2
α-helix	1222-1235	14
β-strand	1238-1244	7	2
α-helix	1248-1259	12
α-helix	1262-1265	4
β-strand	1269-1275	7	2
β-strand	1278-1279	2	13
β-strand	1282-1284	3	13
β-strand	1290-1292	3	13
α-helix	1293-1299	7
α-helix	1306-1308	3
β-strand	1313-1318	6	2
β-strand	1324	1	9
β-strand	1326	1	11
β-strand	1329	1	1

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-5	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JF1cpCasp2	A, B	protein	282	Homo sapiens	P42575 (AlphaFold model)
Acvdvad-cho	C, D	protein	6	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8VP4_1 JF1cpCasp2 (chains A, B)
MHHHHHHGKNHAGSPGCEESAAGKEKLPKMRLPTRSDMICGYACLKGTAAMRNTKRGSWY
IEALAQVFSERACDMHVADMLVKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYLF
PGGGVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDHSTLVT
LFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGVDGKLL
QLQEVFQLFDNANCPSLQNKPKMFFIQACRGDETDRGVDQQD

Sequence of entity 2 (C, D), FASTA

>8VP4_2 AcVDVAD-CHO (chains C, D)
XVDVAD

Primary citation

Reengineering of Circularly Permuted Caspase-2 to Enhance Enzyme Stability and Enable Crystallographic Studies. Fuller, J.L., Shi, K., Pockes, S. et al. ACS Chem Biol (2025) 20:845-857. DOI 10.1021/acschembio.4c00795 · PubMed

Other PDB entries of the same protein (UniProt P42575 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Y8D 1.51 Å, 14-3-3 Sigma in complex with phosphorylated caspase{pS164} peptide
6Y8B 1.54 Å, 14-3-3 Sigma in complex with phosphorylated caspase{pS139} peptide
6S9K 1.6 Å, Structure of 14-3-3 gamma in complex with caspase-2 peptide containing 14-3-3 binding…
1PYO 1.65 Å, Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho
3R5J 1.77 Å, Crystal structure of active caspase-2 bound with Ac-ADVAD-CHO
3R7B 1.8 Å, Caspase-2 bound to one copy of Ac-DVAD-CHO
3R6L 1.9 Å, Caspase-2 T380A bound with Ac-VDVAD-CHO
9C2Y 1.96 Å, Crystal Structure of JF1cpCasp2 in complex with MUR-65
3R6G 2.07 Å, Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO
3R7S 2.25 Å, Crystal Structure of Apo Caspase2
3R7N 2.33 Å, Caspase-2 bound with two copies of Ac-DVAD-CHO
3RJM 2.55 Å, CASPASE2 in complex with chdi ligand 33c

Browse structure collections

About this viewer

MolViewer shows 8VP4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.