1TBB

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Rolipram


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases

Zhang, K.Y.J.Card, G.L.Suzuki, Y.Artis, D.R.Fong, D.Gillette, S.Hsieh, D.Neiman, J.West, B.L.Zhang, C.Milburn, M.V.Kim, S.-H.Schlessinger, J.Bollag, G.

(2004) Mol Cell 15: 279-286

  • DOI: 10.1016/j.molcel.2004.07.005
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Phosphodiesterases (PDEs) comprise a family of enzymes that modulate the immune response, inflammation, and memory, among many other functions. There are three types of PDEs: cAMP-specific, cGMP-specific, and dual-specific. Here we describe the mecha ...

    Phosphodiesterases (PDEs) comprise a family of enzymes that modulate the immune response, inflammation, and memory, among many other functions. There are three types of PDEs: cAMP-specific, cGMP-specific, and dual-specific. Here we describe the mechanism of nucleotide selectivity on the basis of high-resolution co-crystal structures of the cAMP-specific PDE4B and PDE4D with AMP, the cGMP-specific PDE5A with GMP, and the apo-structure of the dual-specific PDE1B. These structures show that an invariant glutamine functions as the key specificity determinant by a "glutamine switch" mechanism for recognizing the purine moiety in cAMP or cGMP. The surrounding residues anchor the glutamine residue in different orientations for cAMP and for cGMP. The PDE1B structure shows that in dual-specific PDEs a key histidine residue may enable the invariant glutamine to toggle between cAMP and cGMP. The structural understanding of nucleotide binding enables the design of new PDE inhibitors that may treat diseases in which cyclic nucleotides play a critical role.


    Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4DA, B332Homo 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)
Explore Q08499 
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS  Q08499
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROL
Query on ROL

Download CCD File 
A, B
ROLIPRAM
C16 H21 N O3
HJORMJIFDVBMOB-LBPRGKRZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4RRKi:  375   nM  BindingDB
4RRIC50:  2630   nM  BindingDB
4RRIC50:  4   nM  BindingDB
4RRKi:  300   nM  BindingDB
4RRKi:  3.799999952316284   nM  BindingDB
4RREC50:  1100   nM  BindingDB
4RRKi:  490   nM  BindingDB
4RRIC50:  390   nM  BindingDB
4RRIC50:  398   nM  BindingDB
4RRIC50:  400   nM  BindingDB
4RRIC50:  1680   nM  BindingDB
4RRIC50:  1600   nM  BindingDB
4RRKi:  382   nM  BindingDB
4RRIC50:  320   nM  BindingDB
4RRIC50:  1000   nM  BindingDB
4RRKi:  930   nM  BindingDB
4RRIC50:  590   nM  BindingDB
4RRIC50:  600   nM  BindingDB
4RRIC50:  550   nM  BindingDB
4RRIC50:  622   nM  BindingDB
4RRIC50:  1000   nM  BindingDB
4RRKi:  58.900001525878906   nM  BindingDB
4RRIC50:  910   nM  BindingDB
4RRIC50:  1430   nM  BindingDB
4RRIC50:  7000   nM  BindingDB
4RRIC50:  1170   nM  BindingDB
4RRIC50:  25   nM  BindingDB
4RRIC50:  1100   nM  BindingDB
4RRIC50:  20   nM  BindingDB
4RRIC50:  2000   nM  BindingDB
4RRIC50:  5000   nM  BindingDB
4RRIC50:  4750   nM  BindingDB
4RRIC50:  1120   nM  BindingDB
4RRIC50:  3690   nM  BindingDB
4RRIC50:  3000   nM  BindingDB
4RRIC50:  3450   nM  BindingDB
4RRIC50:  3500   nM  BindingDB
4RRIC50:  6   nM  BindingDB
4RRIC50:  3410   nM  BindingDB
4RRIC50:  3500   nM  BindingDB
4RRIC50:  31.600000381469727   nM  BindingDB
4RRIC50:  118   nM  BindingDB
4RRIC50:  740   nM  BindingDB
4RRIC50:  33   nM  BindingDB
4RRKi:  1.600000023841858   nM  BindingDB
4RRIC50:  6500   nM  BindingDB
4RRKi:  8460   nM  BindingDB
4RRIC50:  50   nM  BindingDB
4RRIC50:  41   nM  BindingDB
4RRIC50:  60   nM  BindingDB
4RRKi:  1000   nM  BindingDB
4RRIC50:  17000   nM  BindingDB
4RRKi:  4.5   nM  BindingDB
4RRKi:  11   nM  BindingDB
4RRIC50:  550   nM  BindingDB
4RRIC50:  13000   nM  BindingDB
4RRIC50:  500   nM  BindingDB
4RRIC50:  90   nM  BindingDB
4RRIC50:  92   nM  BindingDB
4RRIC50:  70   nM  BindingDB
4RRIC50:  400   nM  BindingDB
4RRIC50:  83   nM  BindingDB
4RRIC50:  80   nM  BindingDB
4RRIC50:  130   nM  BindingDB
4RRIC50:  320   nM  BindingDB
4RRIC50:  140   nM  BindingDB
4RRIC50:  160   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.106α = 90
b = 79.019β = 90
c = 164.548γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance