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Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+

X-ray diffraction
2.203Å resolution
PDB entry 6p0b coloured by chain, front view.
PDB entry 6p0b coloured by chain, side view.
PDB entry 6p0b coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA ligase 1 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 30893.92 Å2
Buried surface area: 8505.97 Å2
Dissociation area: 2,992.82 Å2
Dissociation energy (ΔGdiss): 36.25 kcal/mol
Dissociation entropy (TΔSdiss): 21.93 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120410

Macromolecules

DNA ligase 1
Chain: A
Length: 645 amino acids
Theoretical weight: 71.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P18858 (Residues: 262-904; Coverage: 70%)
Gene name: LIG1
Pfam:
InterPro:
DNA ligase 1 in PDB entry 6p0b, assembly 1, front view.
DNA ligase 1 in PDB entry 6p0b, assembly 1, side view.
DNA ligase 1 in PDB entry 6p0b, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
Representative chains: B
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') in PDB entry 6p0b, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') in PDB entry 6p0b, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') in PDB entry 6p0b, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
Representative chains: C
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') in PDB entry 6p0b, assembly 1, front view.
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') in PDB entry 6p0b, assembly 1, side view.
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') in PDB entry 6p0b, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Representative chains: D
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6p0b, assembly 1, front view.
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6p0b, assembly 1, side view.
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6p0b, assembly 1, top view.
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