› 2hd1

X-ray diffraction
2.23Å resolution

Crystal structure of PDE9 in complex with IBMX

Released:
DOI: 10.2210/pdb2hd1/pdb
PDB entry 2hd1 coloured by chain, front view.
PDB entry 2hd1 coloured by chain, side view.
PDB entry 2hd1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of phosphodiesterase 9 shows orientation variation of inhibitor 3-isobutyl-1-methylxanthine binding.
Huai Q, Wang H, Zhang W, Colman RW, Robinson H, Ke H
Proc Natl Acad Sci U S A 101 9624-9 (2004)
PMID: 15210993

Function and Biology Details

Reaction catalysed: 
Guanosine 3',5'-cyclic phosphate + H(2)O = guanosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131211 (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: 326 amino acids
Theoretical weight: 38.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O76083 (Residues: 241-566; Coverage: 55%)
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 ZN 2 x ZN
Ligand MG 2 x MG
Ligand IBM 2 x IBM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P41212
Unit cell:
a: 103.513Å b: 103.513Å c: 269.727Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.231
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling.
Conti et al. (2007)
6 more

7 mentions without citation

Divergence and convergence in enzyme evolution.
Galperin et al. (2012)
6 more