› 2yy2

X-ray diffraction
2.8Å resolution

Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX

Released:
DOI: 10.2210/pdb2yy2/pdb
PDB entry 2yy2 coloured by chain, front view.
PDB entry 2yy2 coloured by chain, side view.
PDB entry 2yy2 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Handa N, Shirouzu M, Terada T, Omori K, Kotera J, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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:
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: 333 amino acids
Theoretical weight: 39.07 KDa
Source organism: Homo sapiens
Expression system: Not provided
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: RIGAKU
Spacegroup: P41212
Unit cell:
a: 104.27Å b: 104.27Å c: 269.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.206 0.24
Expression system: Not provided

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