3DYS

human phosphodiestrase-5'GMP complex (EP), produced by soaking with 20mM cGMP+20 mM MnCl2+20 mM MgCl2 for 2 hours, and flash-cooled to liquid nitrogen temperature when substrate was still abudant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 3DYS

Classification: HYDROLASE

Total Structure Weight: 78625.70

Macromolecule Entities
Molecule Chains Length Organism Details
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A A, B 329 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: Catalytic domain, UNP residues 242-566
Gene Name(s): PDE9A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5GP
Query on 5GP

A GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IBM
Query on IBM

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

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
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: 2.3 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.186
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.99 α = 90.00
b = 103.99 β = 90.00
c = 269.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-28
  • Released Date: 2008-09-16
  • Deposition author(s): Liu, S., Mansour, M.N., Dillman, K., Perez, J., Danley, D., Menniti, F.

Revision History

  • Version 1_0: 2008-09-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Refinement description, Version format compliance