› 6l84

X-ray diffraction
2.6Å resolution

Complex of DNA polymerase IV and D-DNA duplex

Released:
DOI: 10.2210/pdb6l84/pdb
PDB entry 6l84 coloured by chain, front view.
PDB entry 6l84 coloured by chain, side view.
PDB entry 6l84 coloured by chain, top view.
Source organisms:
Primary publication:
The crystal structure of a natural DNA polymerase complexed with mirror DNA.
An J, Choi J, Hwang D, Park J, Pemble CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR
Chem Commun (Camb) 56 2186-2189 (2020)
PMID: 31971182

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120194 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 360 amino acids
Theoretical weight: 41.33 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.39 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.37 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Unit cell:
a: 52.763Å b: 98.664Å c: 100.769Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.182 0.226
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness.
Dantsu et al. (2021)
4 other articles