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Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with 4-nitrophenol

X-ray diffraction
2.1Å resolution
PDB entry 5m4o coloured by chain, front view.
PDB entry 5m4o coloured by chain, side view.
PDB entry 5m4o coloured by chain, top view.
Source organism: Sphingomonas sp. TTNP3
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Hydroquinone dioxygenase small subunit and Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein
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Multimeric state: hetero tetramer
Accessible surface area: 34538.18 Å2
Buried surface area: 16336.63 Å2
Dissociation area: 1,828.95 Å2
Dissociation energy (ΔGdiss): 14.72 kcal/mol
Dissociation entropy (TΔSdiss): 14.78 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-123731
Assembly 2
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Assembly Name: Hydroquinone dioxygenase small subunit and Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein
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Multimeric state: hetero tetramer
Accessible surface area: 34538.18 Å2
Buried surface area: 16336.63 Å2
Dissociation area: 1,828.95 Å2
Dissociation energy (ΔGdiss): 14.72 kcal/mol
Dissociation entropy (TΔSdiss): 14.78 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-123731
Assembly 3
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Assembly Name: Hydroquinone dioxygenase small subunit and Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein
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Multimeric state: hetero tetramer
Accessible surface area: 35225.19 Å2
Buried surface area: 15740.31 Å2
Dissociation area: 1,825.81 Å2
Dissociation energy (ΔGdiss): 15.28 kcal/mol
Dissociation entropy (TΔSdiss): 14.79 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-123731

Macromolecules

Hydroquinone dioxygenase small subunit
Chains: A, C, E, G
Length: 170 amino acids
Theoretical weight: 18.57 KDa
Source organism: Sphingomonas sp. TTNP3
UniProt:
  • Canonical: F8TW82 (Residues: 1-170; Coverage: 100%)
Gene name: hqdA
Hydroquinone dioxygenase small subunit in PDB entry 5m4o, assembly 1, front view.
Hydroquinone dioxygenase small subunit in PDB entry 5m4o, assembly 1, side view.
Hydroquinone dioxygenase small subunit in PDB entry 5m4o, assembly 1, top view.
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Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein
Chains: B, D, F, H
Length: 341 amino acids
Theoretical weight: 38.24 KDa
Source organism: Sphingomonas sp. TTNP3
UniProt:
  • Canonical: F8TW83 (Residues: 1-341; Coverage: 100%)
Gene name: hqdB
Pfam: Hydroquinone 1,2-dioxygenase large subunit N-terminal
InterPro:
Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein in PDB entry 5m4o, assembly 1, front view.
Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein in PDB entry 5m4o, assembly 1, side view.
Hydroquinone 1,2-dioxygenase large subunit N-terminal domain-containing protein in PDB entry 5m4o, assembly 1, top view.
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