› 3g4g

X-ray diffraction
2.3Å resolution

Crystal structure of human phosphodiesterase 4d with regulatory domain and d155871

Released:
DOI: 10.2210/pdb3g4g/pdb
PDB entry 3g4g coloured by chain, front view.
PDB entry 3g4g coloured by chain, side view.
PDB entry 3g4g coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Burgin AB, Magnusson OT, Singh J, Witte P, Staker BL, Bjornsson JM, Thorsteinsdottir M, Hrafnsdottir S, Hagen T, Kiselyov AS, Stewart LJ, Gurney ME
Nat Biotechnol 28 63-70 (2010)
PMID: 20037581

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-170654 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 421 amino acids
Theoretical weight: 48.37 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08499 (Residues: 299-347, 360-714; Coverage: 50%)
Gene names: DPDE3, PDE4D
Sequence domains:
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand CA 4 x CA
Ligand D71 4 x D71
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P21
Unit cell:
a: 63.129Å b: 75.311Å c: 162.559Å
α: 90° β: 92.43° γ: 90°
R-values:
R R work R free
0.191 0.188 0.257
Expression system: Spodoptera frugiperda

Quick links

Citations

50 review citations

Cognitive dysfunction in psychiatric disorders: characteristics, causes and the quest for improved therapy.
Millan et al. (2012)
49 more

3 mentions without citation

Advances in targeting cyclic nucleotide phosphodiesterases.
Maurice et al. (2014)
2 more