› 7kr4

X-ray diffraction
2.2Å resolution

Human DNA Ligase 1(E346A/E592A) Bound to a nicked DNA substrate control duplex

Released:
DOI: 10.2210/pdb7kr4/pdb
PDB entry 7kr4 coloured by chain, front view.
PDB entry 7kr4 coloured by chain, side view.
PDB entry 7kr4 coloured by chain, top view.
Source organisms:
Primary publication:
High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Williams JS, Tumbale PP, Arana ME, Rana JA, Williams RS, Kunkel TA
OpenAccess logo Nat Commun 12 482 (2021)
PMID: 33473124

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-511619 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase 1 Chain: A
Molecule details ›
Chain: A
Length: 647 amino acids
Theoretical weight: 71.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P18858 (Residues: 262-904; Coverage: 70%)
Gene name: LIG1
Sequence domains:
DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.31 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.09 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ACT 4 x ACT
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: 72.374Å b: 96.556Å c: 114.997Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.162 0.215
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

The base excision repair process: comparison between higher and lower eukaryotes.
Hindi et al. (2021)
5 more