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X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide

X-ray diffraction
2.4Å resolution
PDB entry 1y7v coloured by chain, front view.
PDB entry 1y7v coloured by chain, side view.
PDB entry 1y7v coloured by chain, top view.
Source organism: Homo sapiens
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: Lysosomal acid glucosylceramidase
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Multimeric state: monomeric
Accessible surface area: 18556.76 Å2
Buried surface area: 1877.06 Å2
Dissociation area: 47.13 Å2
Dissociation energy (ΔGdiss): 5.41 kcal/mol
Dissociation entropy (TΔSdiss): 0.6 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-137377
Assembly 2 (preferred)
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Assembly Name: Lysosomal acid glucosylceramidase
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Multimeric state: monomeric
Accessible surface area: 18430.61 Å2
Buried surface area: 1980.78 Å2
Dissociation area: 71.89 Å2
Dissociation energy (ΔGdiss): 10.82 kcal/mol
Dissociation entropy (TΔSdiss): 0.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-137377
Assembly 3
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Assembly Name: Lysosomal acid glucosylceramidase
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Multimeric state: homo tetramer
Accessible surface area: 68134.04 Å2
Buried surface area: 13549.97 Å2
Dissociation area: 1,128.61 Å2
Dissociation energy (ΔGdiss): 12.83 kcal/mol
Dissociation entropy (TΔSdiss): 15.55 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-137379
Assembly 4
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Assembly Name: Lysosomal acid glucosylceramidase
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Multimeric state: homo tetramer
Accessible surface area: 66197.86 Å2
Buried surface area: 15486.15 Å2
Dissociation area: 2,143.63 Å2
Dissociation energy (ΔGdiss): 3.58 kcal/mol
Dissociation entropy (TΔSdiss): 15.82 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-137379
Assembly 5
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Assembly Name: Lysosomal acid glucosylceramidase
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Multimeric state: homo dimer
Accessible surface area: 35247.34 Å2
Buried surface area: 5597.87 Å2
Dissociation area: 870.01 Å2
Dissociation energy (ΔGdiss): 6.31 kcal/mol
Dissociation entropy (TΔSdiss): 14.61 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-137378
Assembly 6
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Assembly Name: Lysosomal acid glucosylceramidase
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Multimeric state: homo dimer
Accessible surface area: 35674.4 Å2
Buried surface area: 5188.17 Å2
Dissociation area: 715.34 Å2
Dissociation energy (ΔGdiss): 1.75 kcal/mol
Dissociation entropy (TΔSdiss): 14.37 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-137378

Macromolecules

Lysosomal acid glucosylceramidase
Chains: A, B
Length: 497 amino acids
Theoretical weight: 55.64 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P04062 (Residues: 40-536; Coverage: 100%)
Gene names: GBA, GBA1, GC, GLUC
Pfam:
InterPro:
CATH:
SCOP:
Lysosomal acid glucosylceramidase in PDB entry 1y7v, assembly 2, front view.
Lysosomal acid glucosylceramidase in PDB entry 1y7v, assembly 2, side view.
Lysosomal acid glucosylceramidase in PDB entry 1y7v, assembly 2, top view.
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