› 3ly2

X-ray diffraction
2.6Å resolution

Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

Released:
DOI: 10.2210/pdb3ly2/pdb
PDB entry 3ly2 coloured by chain, front view.
PDB entry 3ly2 coloured by chain, side view.
PDB entry 3ly2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Water-soluble PDE4 inhibitors for the treatment of dry eye.
Govek SP, Oshiro G, Anzola JV, Beauregard C, Chen J, Coyle AR, Gamache DA, Hellberg MR, Hsien JN, Lerch JM, Liao JC, Malecha JW, Staszewski LM, Thomas DJ, Yanni JM, Noble SA, Shiau AK
Bioorg Med Chem Lett 20 2928-32 (2010)
PMID: 20378348

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 Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 357 amino acids
Theoretical weight: 41.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q07343 (Residues: 324-659; Coverage: 46%)
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 Z72 8 x Z72
Ligand ZN 8 x ZN
Ligand MG 8 x MG
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2221
Unit cell:
a: 214.796Å b: 233.964Å c: 165.258Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.205 0.233
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Ocular surface immunity: homeostatic mechanisms and their disruption in dry eye disease.
Barabino et al. (2012)
1 more

2 mentions without citation

Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such as Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein.
Noone et al. (2021)
1 more