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Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin

X-ray diffraction
1.99Å resolution
PDB entry 2g45 coloured by chain, front view.
PDB entry 2g45 coloured by chain, side view.
PDB entry 2g45 coloured by chain, top view.
Source organism: Homo sapiens
Assemblies composition:
hetero dimer (preferred)
homo dimer
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Ubiquitin carboxyl-terminal hydrolase 5 and Ubiquitin
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Multimeric state: hetero dimer
Accessible surface area: 12199.96 Å2
Buried surface area: 1125.85 Å2
Dissociation area: 506.78 Å2
Dissociation energy (ΔGdiss): -0.25 kcal/mol
Dissociation entropy (TΔSdiss): 10.44 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-143350
Assembly 2
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Assembly Name: Ubiquitin carboxyl-terminal hydrolase 5 and Ubiquitin
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Multimeric state: hetero dimer
Accessible surface area: 12190.92 Å2
Buried surface area: 1010.78 Å2
Dissociation area: 505.39 Å2
Dissociation energy (ΔGdiss): -0.2 kcal/mol
Dissociation entropy (TΔSdiss): 10.43 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-143350
Assembly 3
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Assembly Name: Ubiquitin carboxyl-terminal hydrolase 5
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Multimeric state: homo dimer
Accessible surface area: 13179.89 Å2
Buried surface area: 4250.53 Å2
Dissociation area: 2,125.27 Å2
Dissociation energy (ΔGdiss): 40.7 kcal/mol
Dissociation entropy (TΔSdiss): 11.58 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-155378

Macromolecules

Ubiquitin carboxyl-terminal hydrolase 5
Chains: A, D
Length: 129 amino acids
Theoretical weight: 14.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45974 (Residues: 163-291; Coverage: 15%)
Gene names: ISOT, USP5
Pfam: Zn-finger in ubiquitin-hydrolases and other protein
InterPro:
CATH: Zinc/RING finger domain, C3HC4 (zinc finger)
SCOP: Zf-UBP
Ubiquitin carboxyl-terminal hydrolase 5 in PDB entry 2g45, assembly 1, front view.
Ubiquitin carboxyl-terminal hydrolase 5 in PDB entry 2g45, assembly 1, side view.
Ubiquitin carboxyl-terminal hydrolase 5 in PDB entry 2g45, assembly 1, top view.
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Ubiquitin
Chains: B, E
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Pfam: Ubiquitin family
InterPro:
CATH: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
SCOP: Ubiquitin-related
Ubiquitin in PDB entry 2g45, assembly 1, front view.
Ubiquitin in PDB entry 2g45, assembly 1, side view.
Ubiquitin in PDB entry 2g45, assembly 1, top view.
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