2YY2 | pdb_00002yy2

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

• PDB DOI: https://doi.org/10.2210/pdb2YY2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-04-27 Released: 2007-10-30 
• Deposition Author(s): Handa, N., Shirouzu, M., Terada, T., Omori, K., Kotera, J., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human Phosphodiesterase 9A catalytic domain.

Handa, N., Shirouzu, M., Terada, T., Omori, K., Kotera, J., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.76 kDa 
• Atom Count: 5,512 
• Modeled Residue Count: 650 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	A, B	333	Homo sapiens	Mutation(s): 0  EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76083 (Homo sapiens) Explore O76083  Go to UniProtKB:  O76083
PHAROS:  O76083 GTEx:  ENSG00000160191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IBM	E [auth A], H [auth B]	3-ISOBUTYL-1-METHYLXANTHINE C10 H14 N4 O2 APIXJSLKIYYUKG-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IBM	BindingDB:  2YY2	IC50: min: 1.17e+5, max: 2.00e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.240 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.27	α = 90
b = 104.27	β = 90
c = 269.61	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Handa, N., Shirouzu, M., Terada, T., Omori, K., Kotera, J., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-08-14
  Changes: Database references
• Version 1.4: 2025-04-30
  Changes: Structure summary