› 7rn7

X-ray diffraction
2.4Å resolution

Crystal structure of caspase-3 with inhibitor Ac-VD(Aly)VD-CHO

Released:
DOI: 10.2210/pdb7rn7/pdb
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PDB entry 7rn7 coloured by chain, front view.
PDB entry 7rn7 coloured by chain, side view.
PDB entry 7rn7 coloured by chain, top view.
Source organisms:
Primary publication:
Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314.
Bresinsky M, Strasser JM, Vallaster B, Liu P, McCue WM, Fuller J, Hubmann A, Singh G, Nelson KM, Cuellar ME, Wilmot CM, Finzel BC, Ashe KH, Walters MA, Pockes S
ACS Pharmacol Transl Sci 5 20-40 (2022)
PMID: 35059567

Function and Biology Details

Reaction catalysed: 
Strict requirement for an Asp residue at positions P1 and P4. It has a preferred cleavage sequence of Asp-Xaa-Xaa-Asp-|- with a hydrophobic amino-acid residue at P2 and a hydrophilic amino-acid residue at P3, although Val or Ala are also accepted at this position
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154748 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Caspase-3 subunit p17 Chains: A, C
Molecule details ›
Chains: A, C
Length: 141 amino acids
Theoretical weight: 16.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42574 (Residues: 34-174; Coverage: 51%)
Gene names: CASP3, CPP32
Sequence domains: Caspase domain
Caspase-3 subunit p12 Chains: B, D
Molecule details ›
Chains: B, D
Length: 95 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42574 (Residues: 184-277; Coverage: 34%)
Gene names: CASP3, CPP32
Sequence domains: Caspase domain
Ac-VD(Aly)VD-CHO Chains: F, G

Ligands and Environments

No bound ligands
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 50.509Å b: 68.041Å c: 82.493Å
α: 90° β: 90.608° γ: 90°
R-values:
R R work R free
0.191 0.188 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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Citations

4 review citations

Apoptotic cell death in disease-Current understanding of the NCCD 2023.
Vitale et al. (2023)
3 more

2 mentions without citation

Network pharmacology and experimental verification-based strategy for exploring the mechanisms of luteolin in the treatment of osteosarcoma.
Huang et al. (2023)
1 more

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