› 5hnk

X-ray diffraction
2.22Å resolution

Crystal structure of T5Fen in complex intact substrate and metal ions.

Released:
DOI: 10.2210/pdb5hnk/pdb
PDB entry 5hnk coloured by chain, front view.
PDB entry 5hnk coloured by chain, side view.
PDB entry 5hnk coloured by chain, top view.
Source organisms:
Primary publication:
Direct observation of DNA threading in flap endonuclease complexes.
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ
Nat Struct Mol Biol 23 640-6 (2016)
PMID: 27273516

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118746 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Flap endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 272 amino acids
Theoretical weight: 31.28 KDa
Source organism: Escherichia virus T5
Expression system: Escherichia coli
UniProt:
  • Canonical: P06229 (Residues: 20-291; Coverage: 94%)
Gene names: D15, T5.130, T5p128, exo5
Sequence domains:
Structure domains:
DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3') Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand K 1 x K
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 44.72Å b: 109.94Å c: 127.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.
McLean et al. (2022)
20 other articles

2 mentions without citation

Direct observation of DNA threading in flap endonuclease complexes.
AlMalki et al. (2016)
1 more