› 6bkg

X-ray diffraction
2.4Å resolution

Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation

Released:
DOI: 10.2210/pdb6bkg/pdb
PDB entry 6bkg coloured by chain, front view.
PDB entry 6bkg coloured by chain, side view.
PDB entry 6bkg coloured by chain, top view.
Source organisms:
Primary publication:
Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.
Kaminski AM, Tumbale PP, Schellenberg MJ, Williams RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K
Nat Commun 9 2642 (2018)
PMID: 29980672

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119607 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase 4 Chain: A
Molecule details ›
Chain: A
Length: 621 amino acids
Theoretical weight: 70.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49917 (Residues: 1-620; Coverage: 68%)
Gene name: LIG4
Sequence domains:
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CL 2 x CL
Ligand NA 1 x NA
Ligand EDO 1 x EDO
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 72.657Å b: 102.747Å c: 110.131Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Altered DNA ligase activity in human disease.
Tomkinson et al. (2020)
3 more

3 mentions without citation

Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining.
Kefala Stavridi et al. (2020)
2 more