› 3k4s

X-ray diffraction
2.05Å resolution

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Released:
DOI: 10.2210/pdb3k4s/pdb
PDB entry 3k4s coloured by chain, front view.
PDB entry 3k4s coloured by chain, side view.
PDB entry 3k4s coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Crawley L, Cheng RKY, Wood M, Barker J, Felicetti B, Whittaker M

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 Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 40.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08499 (Residues: 388-715; Coverage: 41%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand 0MO 1 x 0MO
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P4122
Unit cell:
a: 83.217Å b: 83.217Å c: 148.766Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.262
Expression system: Escherichia coli

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