3RJM: CASPASE2

CASPASE2 in complex with chdi ligand 33c. Determined by X-ray diffraction at 2.55 Å resolution. Released 21 Sept 2011.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,307
Mol. weight: 65.89 kDa
Released: 21 Sept 2011

Explore 3RJM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RJM contains 21 α-helices and 38 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: 8 helices, 10 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	161	1	4
β-strand	164-165	2	5

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	211	1	6
β-strand	217-221	5	2
α-helix	228-229	2
β-strand	230-232	3	7
β-strand	236-237	2	7
α-helix	238-250	13
α-helix	256-269	14
β-strand	283	1	4
β-strand	287-290	4	2
β-strand	295	1	1

Chain C: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-22	7
β-strand	26	1	8
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	9
β-strand	117-119	3	9
β-strand	125-127	3	9
α-helix	128-134	7
α-helix	141-143	3
β-strand	148-153	6	2
β-strand	159	1	10
β-strand	161	1	11
β-strand	164	1	6
α-helix	165-167	3

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	210-211	2	5
β-strand	217-221	5	2
β-strand	227	1	10
β-strand	230-232	3	12
β-strand	236-237	2	12
α-helix	238-250	13
α-helix	256-269	14
β-strand	283	1	11
β-strand	287-290	4	2
β-strand	295	1	8

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	403-405	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-2	A, C	protein	169	Homo sapiens	P42575 (AlphaFold model)
Caspase-2	B, D	protein	117	Homo sapiens	P42575 (AlphaFold model)
Peptide inhibitor (ACE)VDV(3PX)D-CHO	E, F	protein	6

Sequence of entity 1 (A, C), FASTA

>3RJM_1 Caspase-2 (chains A, C)
MANKDGPVCLQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDV
DHSTLVTLFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIY
GVDGKLLQLQEVFQLFDNANCPSLQNKPKMFFIQACRGDETDRGVDQQD

Sequence of entity 2 (B, D), FASTA

>3RJM_2 Caspase-2 (chains B, D)
MAGKEKLPKMRLPTRSDMICGYACLKGTAAMRNTKRGSWYIEALAQVFSERACDMHVADM
LVKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYLFPGHPPTAAALEHHHHHH

Sequence of entity 3 (E, F), FASTA

>3RJM_3 Peptide inhibitor (ACE)VDV(3PX)D-CHO (chains E, F)
XVDVXX

Primary citation

Exploiting differences in caspase-2 and -3 S(2) subsites for selectivity: Structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors. Maillard, M.C., Brookfield, F.A., Courtney, S.M. et al. Bioorg Med Chem (2011) 19:5833-5851. DOI 10.1016/j.bmc.2011.08.020 · 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…
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

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