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Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin

X-ray diffraction
2.3Å resolution
PDB entry 3wxf coloured by chain, front view.
PDB entry 3wxf coloured by chain, side view.
PDB entry 3wxf coloured by chain, top view.
Source organisms:
Assembly composition:
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Ubiquitin and Ubiquitin carboxyl-terminal hydrolase CYLD
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Multimeric state: hetero dimer
Accessible surface area: 19769.25 Å2
Buried surface area: 3708.88 Å2
Dissociation area: 1,854.44 Å2
Dissociation energy (ΔGdiss): 17.63 kcal/mol
Dissociation entropy (TΔSdiss): 12.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-123083
Assembly 2 (preferred)
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Assembly Name: Ubiquitin and Ubiquitin carboxyl-terminal hydrolase CYLD
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Multimeric state: hetero dimer
Accessible surface area: 19587.26 Å2
Buried surface area: 3929.15 Å2
Dissociation area: 1,791.1 Å2
Dissociation energy (ΔGdiss): 13.43 kcal/mol
Dissociation entropy (TΔSdiss): 12.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-123083

Macromolecules

Ubiquitin carboxyl-terminal hydrolase CYLD
Chains: A, C
Length: 312 amino acids
Theoretical weight: 35.99 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: E7FEV5 (Residues: 578-780, 850-951; Coverage: 32%)
Gene name: cylda
Pfam: Ubiquitin carboxyl-terminal hydrolase
InterPro:
CATH: Cysteine proteinases
Ubiquitin carboxyl-terminal hydrolase CYLD in PDB entry 3wxf, assembly 2, front view.
Ubiquitin carboxyl-terminal hydrolase CYLD in PDB entry 3wxf, assembly 2, side view.
Ubiquitin carboxyl-terminal hydrolase CYLD in PDB entry 3wxf, assembly 2, top view.
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Ubiquitin
Chains: B, D
Length: 148 amino acids
Theoretical weight: 16.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 533-680; Coverage: 22%)
Gene name: UBC
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 3wxf, assembly 2, front view.
Ubiquitin in PDB entry 3wxf, assembly 2, side view.
Ubiquitin in PDB entry 3wxf, assembly 2, top view.
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