3IAK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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: PDE4DDPDE3
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q08499 (Homo sapiens)
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS  Q08499
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV1
Query on EV1

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.502α = 90
b = 83.502β = 90
c = 148.144γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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