3N3Z

Crystal structure of PDE9A (E406A) mutant in complex with IBMX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 3N3Z

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 77636.44

Macromolecule Entities
Molecule Chains Length Organism Details
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A A, B 326 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: catalytic domain, UNP residues 241-566
Mutation: E406A
Gene Name(s): PDE9A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IBM
Query on IBM

A, B 3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.201
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 104.09 α = 90.00
b = 104.09 β = 90.00
c = 270.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-05-21
  • Released Date: 2011-04-13
  • Deposition author(s): Hou, J., Luo, H.-B., Chen, Y., Xu, J., Zhao, R., Zou, L.

Revision History

  • Version 1_0: 2011-04-13

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance