› 6khy

X-ray diffraction
3.01Å resolution

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219016 (preferred)
Entry contents:
1 distinct polypeptide molecule
6 distinct DNA molecules
Macromolecules (7 distinct):
Probable AP endonuclease Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 301 amino acids
Theoretical weight: 33.84 KDa
Source organism: African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C9C6 (Residues: 1-296; Coverage: 100%)
Gene name: Pret-146
Sequence domains: Xylose isomerase-like TIM barrel
DNA(CCTCGTCGGGGACGCTG) Chain: E
Molecule details ›
Chain: E
Length: 17 nucleotides
Theoretical weight: 5.22 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA(GCAGCGTCACCGACGAGG) Chain: F
Molecule details ›
Chain: F
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA(CCTCGTCGGGGACGCT) Chain: G
Molecule details ›
Chain: G
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA(AGCGTCACCGACGAGG) Chain: H
Molecule details ›
Chain: H
Length: 16 nucleotides
Theoretical weight: 4.93 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA(CCTCGTCGGGGACGC) Chain: I
Molecule details ›
Chain: I
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: African swine fever virus
Expression system: Not provided
DNA (AGCGTCACCGACGAGGC) Chain: J
Molecule details ›
Chain: J
Length: 17 nucleotides
Theoretical weight: 5.22 KDa
Source organism: African swine fever virus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 12 x ZN
Ligand MES 4 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2221
Unit cell:
a: 110.512Å b: 148.504Å c: 178.058Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.249
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Structures and Functional Diversities of ASFV Proteins.
Wang et al. (2021)
10 other articles

1 mention without citation

A unique DNA-binding mode of African swine fever virus AP endonuclease.
Chen et al. (2020)