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Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

X-ray diffraction
1.85Å resolution
PDB entry 2f9r coloured by chain, front view.
PDB entry 2f9r coloured by chain, side view.
PDB entry 2f9r coloured by chain, top view.
Source organism: Loxosceles laeta
Assemblies composition:
monomeric (preferred)
homo tetramer
homo dimer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: monomeric
Accessible surface area: 12271.94 Å2
Buried surface area: 102.76 Å2
Dissociation area: 51.38 Å2
Dissociation energy (ΔGdiss): 11.12 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-184722
Assembly 2 (preferred)
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: monomeric
Accessible surface area: 12494.42 Å2
Buried surface area: 468.11 Å2
Dissociation area: 182.52 Å2
Dissociation energy (ΔGdiss): -6.77 kcal/mol
Dissociation entropy (TΔSdiss): 3.4 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-184722
Assembly 3
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: monomeric
Accessible surface area: 12629.4 Å2
Buried surface area: 470.49 Å2
Dissociation area: 183.33 Å2
Dissociation energy (ΔGdiss): -7.51 kcal/mol
Dissociation entropy (TΔSdiss): 3.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-184722
Assembly 4
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: monomeric
Accessible surface area: 12568.13 Å2
Buried surface area: 461.43 Å2
Dissociation area: 179.02 Å2
Dissociation energy (ΔGdiss): -5.66 kcal/mol
Dissociation entropy (TΔSdiss): 3.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-184722
Assembly 5
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: homo tetramer
Accessible surface area: 41600.84 Å2
Buried surface area: 9874.81 Å2
Dissociation area: 4,545.58 Å2
Dissociation energy (ΔGdiss): 14.31 kcal/mol
Dissociation entropy (TΔSdiss): 41.61 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-184724
Assembly 6
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: homo dimer
Accessible surface area: 22486.96 Å2
Buried surface area: 2850.27 Å2
Dissociation area: 1,318.39 Å2
Dissociation energy (ΔGdiss): -0.82 kcal/mol
Dissociation entropy (TΔSdiss): 13.35 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-184723
Assembly 7
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Assembly Name: Dermonecrotic toxin LlSicTox-alphaIII1i
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Multimeric state: homo dimer
Accessible surface area: 22819.1 Å2
Buried surface area: 3310.35 Å2
Dissociation area: 1,370.33 Å2
Dissociation energy (ΔGdiss): 1.9 kcal/mol
Dissociation entropy (TΔSdiss): 13.38 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-184723

Macromolecules

Dermonecrotic toxin LlSicTox-alphaIII1i
Chains: A, B, C, D
Length: 285 amino acids
Theoretical weight: 32.08 KDa
Source organism: Loxosceles laeta
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8I914 (Residues: 27-311; Coverage: 98%)
InterPro: PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
CATH: Phosphatidylinositol (PI) phosphodiesterase
Dermonecrotic toxin LlSicTox-alphaIII1i in PDB entry 2f9r, assembly 2, front view.
Dermonecrotic toxin LlSicTox-alphaIII1i in PDB entry 2f9r, assembly 2, side view.
Dermonecrotic toxin LlSicTox-alphaIII1i in PDB entry 2f9r, assembly 2, top view.
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