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Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.

X-ray diffraction
3.27Å resolution
PDB entry 6c16 coloured by chain, front view.
PDB entry 6c16 coloured by chain, side view.
PDB entry 6c16 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: 13255.44 Å2
Buried surface area: 3114.2 Å2
Dissociation area: 861.88 Å2
Dissociation energy (ΔGdiss): 6.47 kcal/mol
Dissociation entropy (TΔSdiss): 10.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-533738
Assembly 2
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Multimeric state: hetero trimer
Accessible surface area: 13415.65 Å2
Buried surface area: 3218.07 Å2
Dissociation area: 834.22 Å2
Dissociation energy (ΔGdiss): 7.34 kcal/mol
Dissociation entropy (TΔSdiss): 10.72 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-533738

Macromolecules

S-phase kinase-associated protein 1
Chains: A, B
Length: 165 amino acids
Theoretical weight: 18.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 100%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Pfam:
InterPro:
S-phase kinase-associated protein 1 in PDB entry 6c16, assembly 1, front view.
S-phase kinase-associated protein 1 in PDB entry 6c16, assembly 1, side view.
S-phase kinase-associated protein 1 in PDB entry 6c16, assembly 1, top view.
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Lysine-specific demethylase 2A
Chains: C, F
Length: 47 amino acids
Theoretical weight: 5.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2K7 (Residues: 888-932; Coverage: 4%)
Gene names: CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KDM2A, KIAA1004
Pfam: F-box domain
InterPro:
Lysine-specific demethylase 2A in PDB entry 6c16, assembly 1, front view.
Lysine-specific demethylase 2A in PDB entry 6c16, assembly 1, side view.
Lysine-specific demethylase 2A in PDB entry 6c16, assembly 1, top view.
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Ubiquitin
Chains: D, H
Length: 86 amino acids
Theoretical weight: 9.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-163, 164-228; Coverage: 33%)
Gene name: UBB
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 6c16, assembly 1, front view.
Ubiquitin in PDB entry 6c16, assembly 1, side view.
Ubiquitin in PDB entry 6c16, assembly 1, top view.
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