› 5wqa

X-ray diffraction
2.3Å resolution

Crystal structure of PDE4D catalytic domain complexed with Selaginpulvilins K

Released:
DOI: 10.2210/pdb5wqa/pdb
PDB entry 5wqa coloured by chain, front view.
PDB entry 5wqa coloured by chain, side view.
PDB entry 5wqa coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The discovery, complex crystal structure, and recognition mechanism of a novel natural PDE4 inhibitor from Selaginella pulvinata.
Huang Y, Liu X, Wu D, Tang G, Lai Z, Zheng X, Yin S, Luo HB
Biochem Pharmacol 130 51-59 (2017)
PMID: 28159622

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
Molecule details ›
Chains: A, B
Length: 334 amino acids
Theoretical weight: 38.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q08499 (Residues: 381-714; 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 J20 2 x J20
Ligand ZN 2 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OXFORD DIFFRACTION ENHANCE ULTRA
Spacegroup: P212121
Unit cell:
a: 57.992Å b: 80.784Å c: 163.575Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.217 0.252
Expression system: Escherichia coli BL21

Quick links

Citations

2 review citations

Natural products as modulators of the cyclic-AMP pathway: evaluation and synthesis of lead compounds.
Sengupta et al. (2018)
1 more