1PTW

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis

Structural Biology Knowledgebase: 1PTW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 1PTW

Classification: HYDROLASE

Total Structure Weight: 167492.59

Macromolecule Entities
Molecule Chains Length Organism Details
cAMP-specific phosphodiesterase PDE4D2 A, B, C, D 360 Homo sapiens EC#: 3.1.4.53 IUBMB
Fragment: catalytic domain
Gene Name(s): PDE4D Gene View DPDE3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-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: 0.274
  • R-Value Work: 0.229
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 99.21 α = 90.00
b = 111.23 β = 90.00
c = 159.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-23
  • Released Date: 2003-11-11
  • Deposition author(s): Huai, Q., Colicelli, J., Ke, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4