3DYN

human phosphodiestrase 9 in complex with cGMP (Zn inhibited)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the catalytic mechanism of human phosphodiesterase 9.

Liu, S.Mansour, M.N.Dillman, K.S.Perez, J.R.Danley, D.E.Aeed, P.A.Simons, S.P.Lemotte, P.K.Menniti, F.S.

(2008) Proc Natl Acad Sci U S A 105: 13309-13314

  • DOI: 10.1073/pnas.0708850105
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The phosphodiesterases (PDEs) are metal ion-dependent enzymes that regulate cellular signaling by metabolic inactivation of the ubiquitous second messengers cAMP and cGMP. In this role, the PDEs are involved in many biological and metabolic processes ...

    The phosphodiesterases (PDEs) are metal ion-dependent enzymes that regulate cellular signaling by metabolic inactivation of the ubiquitous second messengers cAMP and cGMP. In this role, the PDEs are involved in many biological and metabolic processes and are proven targets of successful drugs for the treatments of a wide range of diseases. However, because of the rapidity of the hydrolysis reaction, an experimental knowledge of the enzymatic mechanisms of the PDEs at the atomic level is still lacking. Here, we report the structures of reaction intermediates accumulated at the reaction steady state in PDE9/crystal and preserved by freeze-trapping. These structures reveal the catalytic process of a PDE and explain the substrate specificity of PDE9 in an actual reaction and the cation requirements of PDEs in general.


    Organizational Affiliation

    Pfizer Global Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA. shenping.liu@pfizer.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
Find proteins for O76083 (Homo sapiens)
Go to UniProtKB:  O76083
NIH Common Fund Data Resources
PHAROS  O76083
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download CCD File 
A, B
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
IBM
Query on IBM

Download CCD File 
B
3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.857α = 90
b = 103.857β = 90
c = 270.118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance