› 3v4k

X-ray diffraction
1.38Å resolution

First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G

Released:
DOI: 10.2210/pdb3v4k/pdb
PDB entry 3v4k coloured by chain, front view.
PDB entry 3v4k coloured by chain, side view.
PDB entry 3v4k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.
Li M, Shandilya SM, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS
ACS Chem Biol 7 506-17 (2012)
PMID: 22181350

Function and Biology Details

Reaction catalysed: 
Cytosine in single-stranded DNA + H(2)O = uracil in single-stranded DNA + NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-190764 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA dC->dU-editing enzyme APOBEC-3G Chains: A, B
Molecule details ›
Chains: A, B
Length: 203 amino acids
Theoretical weight: 23.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9HC16 (Residues: 191-380; Coverage: 50%)
Gene names: APOBEC3G, MDS019
Sequence domains: APOBEC-like C-terminal domain

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand MG 2 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 68.19Å b: 72.17Å c: 96.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.183 0.215
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

18 review citations

APOBECs and virus restriction.
Harris et al. (2015)
17 more

17 mentions without citation

APOBEC Enzymes as Targets for Virus and Cancer Therapy.
Olson et al. (2018)
16 more