› 6fet

X-ray diffraction
1.88Å resolution

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439

Released:
DOI: 10.2210/pdb6fet/pdb
PDB entry 6fet coloured by chain, front view.
PDB entry 6fet coloured by chain, side view.
PDB entry 6fet coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Singh AK, Brown DG

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: 364 amino acids
Theoretical weight: 41.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 381-740; Coverage: 45%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

8 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand EDO 67 x EDO
Ligand PEG 4 x PEG
Ligand D68 4 x D68
Ligand EPE 5 x EPE
Ligand NI 2 x NI
Ligand PG4 2 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 97.19Å b: 110.71Å c: 161.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.199
Expression system: Escherichia coli BL21(DE3)

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