3IAK

Crystal structure of human phosphodiesterase 4d (PDE4d) with papaverine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human phosphodiesterase 4d (PDE4d) with papaverine.

Cheng, R.K.Y.Crawley, L.Barker, J.Wood, M.Felicetti, B.Whittaker, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A
349Homo sapiensMutation(s): 0 
Gene Names: PDE4D (DPDE3)
EC: 3.1.4.53
Find proteins for Q08499 (Homo sapiens)
Go to Gene View: PDE4D
Go to UniProtKB:  Q08499
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV1
Query on EV1

Download SDF File 
Download CCD File 
A
1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE
C20 H21 N O4
XQYZDYMELSJDRZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EV1Ki: 8821.4 - >10000 nM (85) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.502α = 90.00
b = 83.502β = 90.00
c = 148.144γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
REFMACrefinement
DNAdata collection
CrystalCleardata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance