1OBZ

Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm

Kang, B.S.Cooper, D.R.Devedjiev, Y.Derewenda, U.Derewenda, Z.S.

(2003) Structure 11: 845

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. ...

    Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SYNTENIN 1
A, B
166Homo sapiensMutation(s): 0 
Gene Names: SDCBP (MDA9, SYCL)
Find proteins for O00560 (Homo sapiens)
Go to Gene View: SDCBP
Go to UniProtKB:  O00560
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTERLEUKIN 5 RECEPTOR ALPHA
P
8Homo sapiensMutation(s): 0 
Gene Names: IL5RA (IL5R)
Find proteins for Q01344 (Homo sapiens)
Go to Gene View: IL5RA
Go to UniProtKB:  Q01344
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.485α = 90.00
b = 48.172β = 120.24
c = 74.996γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance