› 8ile

X-ray diffraction
3Å resolution

The crystal structure of dGTPalphaSe-Rp:DNApre-II:Pol X substrate ternary complex

Released:
DOI: 10.2210/pdb8ile/pdb
PDB entry 8ile coloured by chain, front view.
PDB entry 8ile coloured by chain, side view.
PDB entry 8ile coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z
OpenAccess logo Int J Mol Sci 24 (2023)
PMID: 37958741

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238589 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Repair DNA polymerase X Chains: A, B
Molecule details ›
Chains: A, B
Length: 176 amino acids
Theoretical weight: 20.47 KDa
Source organism: African swine fever virus BA71V
Expression system: Escherichia coli
UniProt:
  • Canonical: P42494 (Residues: 1-174; Coverage: 100%)
Gene names: Ba71V-97, O174L
Sequence domains:
DNA (5'-D(*CP*TP*GP*GP*AP*TP*CP*CP*A)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 4 x MN
Ligand 7Q6 2 x 7Q6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 59.481Å b: 77.382Å c: 111.353Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.22 0.284
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 mentions without citation

Identification of amino acid residues of rat angiotensin II receptor for ligand binding by site directed mutagenesis.
Yamano et al. (1992)
1 more