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RCR E3 ligase E2-Ubiquitin transthiolation intermediate

X-ray diffraction
2.58Å resolution
PDB entry 6t7f coloured by chain, front view.
PDB entry 6t7f coloured by chain, side view.
PDB entry 6t7f coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 22440.05 Å2
Buried surface area: 3514.75 Å2
Dissociation area: 1,757.38 Å2
Dissociation energy (ΔGdiss): -7.93 kcal/mol
Dissociation entropy (TΔSdiss): 23.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-131074

Macromolecules

E3 ubiquitin-protein ligase MYCBP2
Chain: A
Length: 261 amino acids
Theoretical weight: 29.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75592 (Residues: 4423-4678; Coverage: 6%)
Gene names: KIAA0916, MYCBP2, PAM
InterPro:
E3 ubiquitin-protein ligase MYCBP2 in PDB entry 6t7f, assembly 1, front view.
E3 ubiquitin-protein ligase MYCBP2 in PDB entry 6t7f, assembly 1, side view.
E3 ubiquitin-protein ligase MYCBP2 in PDB entry 6t7f, assembly 1, top view.
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Ubiquitin-conjugating enzyme E2 D3
Chain: B
Length: 150 amino acids
Theoretical weight: 16.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 2-147; Coverage: 99%)
Gene names: UBC5C, UBCH5C, UBE2D3
Pfam: Ubiquitin-conjugating enzyme
InterPro:
Ubiquitin-conjugating enzyme E2 D3 in PDB entry 6t7f, assembly 1, front view.
Ubiquitin-conjugating enzyme E2 D3 in PDB entry 6t7f, assembly 1, side view.
Ubiquitin-conjugating enzyme E2 D3 in PDB entry 6t7f, assembly 1, top view.
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Ubiquitin
Chain: C
Length: 73 amino acids
Theoretical weight: 8.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-681; Coverage: 11%)
Gene name: UBC
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 6t7f, assembly 1, front view.
Ubiquitin in PDB entry 6t7f, assembly 1, side view.
Ubiquitin in PDB entry 6t7f, assembly 1, top view.
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