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Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution

X-ray diffraction
1.5Å resolution
PDB entry 4gz1 coloured by chain, front view.
PDB entry 4gz1 coloured by chain, side view.
PDB entry 4gz1 coloured by chain, top view.
Source organism: Mus musculus
Assemblies composition:
hetero dimer
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
1 distinct DNA molecule

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Assemblies

Assembly 1
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Assembly Name: Tyrosyl-DNA phosphodiesterase 2 and DNA
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Multimeric state: hetero dimer
Accessible surface area: 13134.22 Å2
Buried surface area: 1330.9 Å2
Dissociation area: 504.96 Å2
Dissociation energy (ΔGdiss): 8.43 kcal/mol
Dissociation entropy (TΔSdiss): 9.34 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117567
Assembly 2
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Assembly Name: Tyrosyl-DNA phosphodiesterase 2 and DNA
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Multimeric state: hetero dimer
Accessible surface area: 12587.74 Å2
Buried surface area: 1188.12 Å2
Dissociation area: 462.41 Å2
Dissociation energy (ΔGdiss): 9.13 kcal/mol
Dissociation entropy (TΔSdiss): 9.33 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117567
Assembly 3 (preferred)
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Assembly Name: Tyrosyl-DNA phosphodiesterase 2 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 24553.73 Å2
Buried surface area: 3687.24 Å2
Dissociation area: 585.5 Å2
Dissociation energy (ΔGdiss): 2.25 kcal/mol
Dissociation entropy (TΔSdiss): 13.08 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-117568

Macromolecules

Tyrosyl-DNA phosphodiesterase 2
Chains: A, B
Length: 256 amino acids
Theoretical weight: 28.89 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-370; Coverage: 68%)
Gene names: Tdp2, Ttrap
Pfam: Endonuclease/Exonuclease/phosphatase family
InterPro:
CATH: Endonuclease/exonuclease/phosphatase
Tyrosyl-DNA phosphodiesterase 2 in PDB entry 4gz1, assembly 3, front view.
Tyrosyl-DNA phosphodiesterase 2 in PDB entry 4gz1, assembly 3, side view.
Tyrosyl-DNA phosphodiesterase 2 in PDB entry 4gz1, assembly 3, top view.
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DNA chains C, D
Name: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
Representative chains: C, D
Source organism: Mus musculus [10090]
Expression system: Not provided
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') in PDB entry 4gz1, assembly 3, front view.
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') in PDB entry 4gz1, assembly 3, side view.
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') in PDB entry 4gz1, assembly 3, top view.
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