1PYO: Human Caspase-2

Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho. Determined by X-ray diffraction at 1.65 Å resolution. Released 26 Aug 2003.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae (Baker's yeast)
Chains: 6
Atoms: 4,606
Mol. weight: 62.6 kDa
Released: 26 Aug 2003

Explore 1PYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PYO contains 24 α-helices and 40 β-strands across 6 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-22	7
α-helix	23-25	3
β-strand	26	1	1
β-strand	35-41	7	2
α-helix	57-70	14
β-strand	73-79	7	2
α-helix	83-94	12
α-helix	97-100	4
β-strand	104-110	7	2
β-strand	113-114	2	3
β-strand	117-119	3	3
β-strand	125-127	3	3
α-helix	128-134	7
α-helix	141-143	3
β-strand	148-153	6	2
β-strand	159	1	4
α-helix	160	1
β-strand	161	1	5
β-strand	164-165	2	6

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	210-211	2	7
β-strand	217-221	5	2
β-strand	227	1	4
α-helix	228-229	2
β-strand	230-232	3	8
β-strand	236-237	2	8
α-helix	238-250	13
α-helix	256-268	13
β-strand	283	1	5
β-strand	287-290	4	2
β-strand	295	1	1

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-22	7
α-helix	23-25	3
β-strand	26	1	9
β-strand	35-41	7	2
α-helix	57-70	14
β-strand	73-79	7	2
α-helix	83-94	12
α-helix	97-101	5
β-strand	104-110	7	2
β-strand	113-114	2	10
β-strand	117-119	3	10
β-strand	125-127	3	10
α-helix	128-134	7
α-helix	141-143	3
β-strand	148-153	6	2
β-strand	159	1	11
β-strand	161	1	12
β-strand	164-165	2	7
α-helix	166-167	2

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	210-211	2	6
β-strand	217-221	5	2
β-strand	227	1	11
α-helix	228-229	2
β-strand	230-232	3	13
β-strand	236-237	2	13
α-helix	238-250	13
α-helix	256-269	14
β-strand	283	1	12
β-strand	287-290	4	2
β-strand	295	1	9

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	403-405	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-2	A, C	protein	167	Homo sapiens	P42575 (AlphaFold model)
Caspase-2	B, D	protein	105	Homo sapiens	P42575 (AlphaFold model)
Acetyl-leu-asp-glu-ser-asj	E, F	protein	6	Saccharomyces cerevisiae (Baker's yeast)	P36114 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1PYO_1 Caspase-2 (chains A, C)
NKDGPVCLQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDH
STLVTLFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGV
DGKLLQLQEVFQLFDNANCPSLQNKPKMFFIQACRGDETDRGVDQQD

Sequence of entity 2 (B, D), FASTA

>1PYO_2 Caspase-2 (chains B, D)
AGKEKLPKMRLPTRSDMICGYACLKGTAAMRNTKRGSWYIEALAQVFSERACDMHVADML
VKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYLFPGHPPT

Sequence of entity 3 (E, F), FASTA

>1PYO_3 ACETYL-LEU-ASP-GLU-SER-ASJ (chains E, F)
XLDESX

Primary citation

Crystal structure of caspase-2, apical initiator of the intrinsic apoptotic pathway. Schweizer, A., Briand, C., Grutter, M.G. J Biol Chem (2003) 278:42441-42447. DOI 10.1074/jbc.M304895200 · 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
8VP4 1.51 Å, Crystal Structure of JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO
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…
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

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