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Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States

X-ray diffraction
3Å resolution
PDB entry 3l2p coloured by chain, front view.
PDB entry 3l2p coloured by chain, side view.
PDB entry 3l2p coloured by chain, top view.
Source organism: Homo sapiens
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 3 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 29878.73 Å2
Buried surface area: 7539.43 Å2
Dissociation area: 1,162.54 Å2
Dissociation energy (ΔGdiss): 21.42 kcal/mol
Dissociation entropy (TΔSdiss): 10.16 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116515

Macromolecules

DNA ligase 3
Chain: A
Length: 579 amino acids
Theoretical weight: 65.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49916 (Residues: 257-833; Coverage: 57%)
Gene name: LIG3
Pfam:
InterPro:
CATH:
DNA ligase 3 in PDB entry 3l2p, assembly 1, front view.
DNA ligase 3 in PDB entry 3l2p, assembly 1, side view.
DNA ligase 3 in PDB entry 3l2p, assembly 1, top view.
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DNA chain B
Name: 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'
Representative chains: B
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' in PDB entry 3l2p, assembly 1, front view.
5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' in PDB entry 3l2p, assembly 1, side view.
5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' in PDB entry 3l2p, assembly 1, top view.
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DNA chain C
Name: 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'
Representative chains: C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3' in PDB entry 3l2p, assembly 1, front view.
5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3' in PDB entry 3l2p, assembly 1, side view.
5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3' in PDB entry 3l2p, assembly 1, top view.
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DNA chain D
Name: 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3'
Representative chains: D
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 22 nucleotides
Theoretical weight: 6.68 KDa
5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3' in PDB entry 3l2p, assembly 1, front view.
5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3' in PDB entry 3l2p, assembly 1, side view.
5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3' in PDB entry 3l2p, assembly 1, top view.
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