› 3itu

X-ray diffraction
1.58Å resolution

hPDE2A catalytic domain complexed with IBMX

Released:
DOI: 10.2210/pdb3itu/pdb
PDB entry 3itu coloured by chain, front view.
PDB entry 3itu coloured by chain, side view.
PDB entry 3itu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.
Pandit J, Forman MD, Fennell KF, Dillman KS, Menniti FS
Proc Natl Acad Sci U S A 106 18225-30 (2009)
PMID: 19828435

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-126260 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cGMP-dependent 3',5'-cyclic phosphodiesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 345 amino acids
Theoretical weight: 40.23 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00408 (Residues: 579-919; Coverage: 36%)
Gene name: PDE2A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand IBM 4 x IBM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P1
Unit cell:
a: 55.815Å b: 73.287Å c: 91.532Å
α: 109.3° β: 88.8° γ: 89°
R-values:
R R work R free
0.177 0.174 0.233
Expression system: Spodoptera frugiperda

Quick links

Citations

26 review citations

cGMP-dependent protein kinases and cGMP phosphodiesterases in nitric oxide and cGMP action.
Francis et al. (2010)
25 more

5 mentions without citation

Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.
Pandit et al. (2009)
4 more