2WEY

Human PDE-papaverine complex obtained by ligand soaking of cross- linked protein crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cross-Linking of Protein Crystals as an Aid in the Generation of Binary Protein-Ligand Crystal Complexes, Exemplified by the Human Pde10A-Papaverine Structure.

Andersen, O.A.Schonfeld, D.L.Toogood-Johnson, I.Felicetti, B.Albrecht, C.Fryatt, T.Whittaker, M.Hallett, D.Barker, J.

(2009) Acta Crystallogr D Biol Crystallogr 65: 872

  • DOI: 10.1107/S0907444909017855
  • Primary Citation of Related Structures:  
    2WEY

  • PubMed Abstract: 
  • Protein crystallography has proven to be an effective method of obtaining high-resolution structures of protein-ligand complexes. However, in certain cases only apoprotein structures are readily available and the generation of crystal complexes is mo ...

    Protein crystallography has proven to be an effective method of obtaining high-resolution structures of protein-ligand complexes. However, in certain cases only apoprotein structures are readily available and the generation of crystal complexes is more problematic. Some crystallographic systems are not amenable to soaking of ligands owing to crystal-packing effects and many protein-ligand complexes do not crystallize under the same conditions as used for the apoprotein. Using crystals of human phosphodiesterase 10a (hPDE10a) as an example of such a challenging crystallographic system, the structure of the complex with papaverine was obtained to 2.8 A resolution using protein crystals cross-linked by glutaraldehyde prior to soaking of the ligand. Inspection of the electron-density maps suggested that the correct mode of binding was obtained in one of the two monomers in the asymmetric unit and inspection of crystal-packing contacts explained why cocrystallization experiments and soaking of crystals that were not cross-linked were unsuccessful.


    Organizational Affiliation

    Evotec UK Ltd, Abingdon, Oxfordshire OX14 4SA, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP AND CAMP-INHIBITED CGMP 3', 5'-CYCLIC PHOSPHODIESTERASEAB343Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
NIH Common Fund Data Resources
PHAROS  Q9Y233
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV1
Query on EV1

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

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-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 %)
EV1IC50:  76   nM  BindingDB
EV1IC50:  36   nM  BindingDB
EV1IC50:  17   nM  BindingDB
EV1Ki:  17   nM  BindingDB
EV1IC50:  210   nM  BindingDB
EV1IC50:  36   nM  BindingDB
EV1IC50 :  76   nM  PDBBind
EV1IC50:  21   nM  BindingDB
EV1IC50:  40   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.84α = 90
b = 81.57β = 90
c = 157.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2017-07-05
    Changes: Data collection