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Structure of EndoMS-dsDNA1'' complex

X-ray diffraction
2.6Å resolution
PDB entry 5gkg coloured by chain, front view.
PDB entry 5gkg coloured by chain, side view.
PDB entry 5gkg coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Endonuclease NucS and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 22612.29 Å2
Buried surface area: 14059.45 Å2
Dissociation area: 4,211.71 Å2
Dissociation energy (ΔGdiss): 67.95 kcal/mol
Dissociation entropy (TΔSdiss): 14.36 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118703

Macromolecules

Endonuclease NucS
Chains: A, B
Length: 252 amino acids
Theoretical weight: 28.6 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JER9 (Residues: 1-252; Coverage: 100%)
Gene names: TK1898, nucS
Pfam:
InterPro:
Endonuclease NucS in PDB entry 5gkg, assembly 1, front view.
Endonuclease NucS in PDB entry 5gkg, assembly 1, side view.
Endonuclease NucS in PDB entry 5gkg, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3')
Representative chains: C
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3') in PDB entry 5gkg, assembly 1, front view.
DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3') in PDB entry 5gkg, assembly 1, side view.
DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3') in PDB entry 5gkg, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3')
Representative chains: D
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.68 KDa
DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3') in PDB entry 5gkg, assembly 1, front view.
DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3') in PDB entry 5gkg, assembly 1, side view.
DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3') in PDB entry 5gkg, assembly 1, top view.
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