› 4y8c

X-ray diffraction
2.7Å resolution

Crystal structure of phosphodiesterase 9 in complex with (S)-C33

Released:
DOI: 10.2210/pdb4y8c/pdb
PDB entry 4y8c coloured by chain, front view.
PDB entry 4y8c coloured by chain, side view.
PDB entry 4y8c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor.
Huang M, Shao Y, Hou J, Cui W, Liang B, Huang Y, Li Z, Wu Y, Zhu X, Liu P, Wan Y, Ke H, Luo HB
Mol Pharmacol 88 836-45 (2015)
PMID: 26316540

Function and Biology Details

Reaction catalysed: 
Guanosine 3',5'-cyclic phosphate + H(2)O = guanosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131212 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A Chains: A, B
Molecule details ›
Chains: A, B
Length: 533 amino acids
Theoretical weight: 61.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O76083 (Residues: 1-593; Coverage: 90%)
Gene name: PDE9A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand 49D 2 x 49D
Ligand ZN 2 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P41212
Unit cell:
a: 104.719Å b: 104.719Å c: 270.274Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.231
Expression system: Escherichia coli BL21

Quick links

Citations

4 review citations

Biopharmaceuticals from microorganisms: from production to purification.
Jozala et al. (2016)
3 more

2 mentions without citation

A Perspective on Natural and Nature-Inspired Small Molecules Targeting Phosphodiesterase 9 (PDE9): Chances and Challenges against Neurodegeneration.
Ribaudo et al. (2021)
1 more