› 3o0j

X-ray diffraction
1.95Å resolution

PDE4B In complex with ligand an2898

Released:
DOI: 10.2210/pdb3o0j/pdb
PDB entry 3o0j coloured by chain, front view.
PDB entry 3o0j coloured by chain, side view.
PDB entry 3o0j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Boron-based phosphodiesterase inhibitors show novel binding of boron to PDE4 bimetal center.
Freund YR, Akama T, Alley MR, Antunes J, Dong C, Jarnagin K, Kimura R, Nieman JA, Maples KR, Plattner JJ, Rock F, Sharma R, Singh R, Sanders V, Zhou Y
FEBS Lett 586 3410-4 (2012)
PMID: 22841723

Function and Biology Details

Reaction catalysed: 
Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170460 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4B Chain: A
Molecule details ›
Chain: A
Length: 323 amino acids
Theoretical weight: 37.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q07343 (Residues: 334-656; Coverage: 44%)
Gene names: DPDE4, PDE4B
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand 3OJ 1 x 3OJ
Ligand EDO 14 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P43212
Unit cell:
a: 53.611Å b: 53.611Å c: 229.014Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.184 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

The unique chemistry of benzoxaboroles: current and emerging applications in biotechnology and therapeutic treatments.
Liu et al. (2014)
15 more

2 mentions without citation

Reactive chemistry for covalent probe and therapeutic development.
Grams et al. (2022)
1 more