› 3iak

X-ray diffraction
2.8Å resolution

Crystal structure of human phosphodiesterase 4d (PDE4d) with papaverine.

Released:
DOI: 10.2210/pdb3iak/pdb
PDB entry 3iak coloured by chain, front view.
PDB entry 3iak coloured by chain, side view.
PDB entry 3iak coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Cheng RKY, Crawley L, Barker J, Wood M, 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 MG 1 x MG
Ligand EV1 1 x EV1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P4122
Unit cell:
a: 83.502Å b: 83.502Å c: 148.144Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.239 0.291
Expression system: Escherichia coli

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