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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg)

Electron Microscopy
3.16Å resolution
PDB entry 9b5t coloured by chain, front view.
PDB entry 9b5t coloured by chain, side view.
PDB entry 9b5t coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
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: 48842.91 Å2
Buried surface area: 4369.62 Å2
Dissociation area: 1,598.29 Å2
Dissociation energy (ΔGdiss): 6.91 kcal/mol
Dissociation entropy (TΔSdiss): 13.11 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-131720

Macromolecules

Ubiquitin-activating enzyme E1 1
Chain: A
Length: 1001 amino acids
Theoretical weight: 111.76 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O94609 (Residues: 13-1012; Coverage: 99%)
Gene names: SPBC1604.21c, SPBC211.09, ptr3
Pfam:
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5t, assembly 1, front view.
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5t, assembly 1, side view.
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5t, assembly 1, top view.
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Ubiquitin-conjugating enzyme E2 4
Chain: C
Length: 153 amino acids
Theoretical weight: 17.04 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46595 (Residues: 1-147; Coverage: 100%)
Gene names: SPBC119.02, ubc4
Pfam: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5t, assembly 1, front view.
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5t, assembly 1, side view.
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5t, assembly 1, top view.
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Ubiquitin
Chain: D
Length: 79 amino acids
Theoretical weight: 8.77 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CH07 (Residues: 1-75; Coverage: 59%)
Gene names: SPAC1805.12c, ubi2, uep1
Pfam: Ubiquitin family
Ubiquitin in PDB entry 9b5t, assembly 1, front view.
Ubiquitin in PDB entry 9b5t, assembly 1, side view.
Ubiquitin in PDB entry 9b5t, assembly 1, top view.
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