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MolNFT v1 · #34581 · protein

Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis

2DKO: “Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis”. X-ray diffraction, 1 ligand (0QE). MolNFT v1 #34581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
2DKO
Type
protein
Length
253 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Caspase-3; Phq-asp-glu-val-asp-chloromethylketone
EC
3.4.22.-
UniProt
P42574
Ligands
0QE

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACaspase-3 (EC 3.4.22.-)protein14627% helix, 29% strandP42574
BCaspase-3 (EC 3.4.22.-)protein10330% helix, 17% strandP42574
IPhq-asp-glu-val-asp-chloromethylketoneprotein40% helix, 50% strand—

Ligands and binding sites

  • 0QE · Chloromethane · ion · chains A, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

3 interfaces between chains.

  • A–B · 2236 Ų buried · 35 hydrogen bonds · protein-protein
  • B–I · 405 Ų buried · 9 hydrogen bonds · protein-protein
  • A–I · 225 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

  • 2DKO · Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure… · the same entry in another collection · chain A against A, TM-score 1.00
  • P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain A against A, TM-score 0.99

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