› 6r5d

X-ray diffraction
1.95Å resolution

Crystal structure of the Pri1 subunit of human primase bound to dATP

Released:
DOI: 10.2210/pdb6r5d/pdb
PDB entry 6r5d coloured by chain, front view.
PDB entry 6r5d coloured by chain, side view.
PDB entry 6r5d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Holzer S, Rzechorzek NJ, Short IR, Jenkyn-Bedford M, Pellegrini L, Kilkenny ML
ACS Chem Biol 14 1904-1912 (2019)
PMID: 31479243

Function and Biology Details

Reaction catalysed: 
SsDNA + n NTP = ssDNA/pppN(pN)(n-1) hybrid + (n-1) diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155973 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA primase small subunit Chains: A, E
Molecule details ›
Chains: A, E
Length: 410 amino acids
Theoretical weight: 48.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49642 (Residues: 1-407; Coverage: 97%)
Gene name: PRIM1
Sequence domains: DNA primase small subunit

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand MN 4 x MN
Ligand DTP 2 x DTP
Ligand EDO 11 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2221
Unit cell:
a: 110.52Å b: 117.29Å c: 151.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.214
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Transcription and Translation Inhibitors in Cancer Treatment.
Laham-Karam et al. (2020)
4 more

3 mentions without citation

Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Holzer et al. (2019)
2 more