› 6f8x

X-ray diffraction
1.95Å resolution

Crystal structure of the PDE4D catalytic domain in complex with GEBR-26g

Released:
DOI: 10.2210/pdb6f8x/pdb
PDB entry 6f8x coloured by chain, front view.
PDB entry 6f8x coloured by chain, side view.
PDB entry 6f8x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Prosdocimi T, Mollica L, Donini S, Semrau MS, Lucarelli AP, Aiolfi E, Cavalli A, Storici P, Alfei S, Brullo C, Bruno O, Parisini E
Biochemistry 57 2876-2888 (2018)
PMID: 29652483

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170655 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 39.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 380-715; Coverage: 42%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 4 x MG
Ligand D08 2 x D08
Ligand EDO 2 x EDO
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 98.547Å b: 119.82Å c: 64.502Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.166 0.205
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

Insight into Inhibitory Mechanism of PDE4D by Dietary Polyphenols Using Molecular Dynamics Simulations and Free Energy Calculations.
Furlan et al. (2021)
2 more