› › Structure analysis

TRIM23 RING domain in complex with UbcH5-Ub

X-ray diffraction
2.278Å resolution
PDB entry 5vzw coloured by chain, front view.
PDB entry 5vzw coloured by chain, side view.
PDB entry 5vzw coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero hexamer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexamer
Accessible surface area: 26387.58 Å2
Buried surface area: 9005.69 Å2
Dissociation area: 4,495.24 Å2
Dissociation energy (ΔGdiss): -8.36 kcal/mol
Dissociation entropy (TΔSdiss): 57.76 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-143298

Macromolecules

Ubiquitin-conjugating enzyme E2 D2
Chains: A, B
Length: 147 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Pfam: Ubiquitin-conjugating enzyme
InterPro:
Ubiquitin-conjugating enzyme E2 D2 in PDB entry 5vzw, assembly 1, front view.
Ubiquitin-conjugating enzyme E2 D2 in PDB entry 5vzw, assembly 1, side view.
Ubiquitin-conjugating enzyme E2 D2 in PDB entry 5vzw, assembly 1, top view.
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Ubiquitin
Chains: C, D
Length: 79 amino acids
Theoretical weight: 8.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 5vzw, assembly 1, front view.
Ubiquitin in PDB entry 5vzw, assembly 1, side view.
Ubiquitin in PDB entry 5vzw, assembly 1, top view.
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E3 ubiquitin-protein ligase TRIM23
Chains: F, G
Length: 123 amino acids
Theoretical weight: 13.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36406 (Residues: 1-123; Coverage: 21%)
Gene names: ARD1, ARFD1, RNF46, TRIM23
Pfam: RING-type zinc-finger
InterPro:
E3 ubiquitin-protein ligase TRIM23 in PDB entry 5vzw, assembly 1, front view.
E3 ubiquitin-protein ligase TRIM23 in PDB entry 5vzw, assembly 1, side view.
E3 ubiquitin-protein ligase TRIM23 in PDB entry 5vzw, assembly 1, top view.
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