4Z33

Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the Frizzled 7 C-terminal fragment and PIP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the Frizzled 7 C-terminal fragment and PIP2

Egea-Jimenez, A.L.Gallardo, R.Garcia-Pino, A.Ivarsson, Y.Wawrzyniak, A.M.Kashyap, R.Loris, R.Schymkowitz, J.Rousseau, F.Zimmermann, P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syntenin-1
A, B
166Homo sapiensMutation(s): 0 
Gene Names: SDCBPMDA9SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens)
Explore O00560 
Go to UniProtKB:  O00560
PHAROS:  O00560
GTEx:  ENSG00000137575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00560
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LYS-GLY-GLU-THR-ALA-VAL
C, D
6Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75084 (Homo sapiens)
Explore O75084 
Go to UniProtKB:  O75084
PHAROS:  O75084
GTEx:  ENSG00000155760 
Entity Groups  
UniProt GroupO75084
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IP2
Query on IP2

Download Ideal Coordinates CCD File 
H [auth A]D-MYO-INOSITOL-4,5-BISPHOSPHATE
C6 H14 O12 P2
MCKAJXMRULSUKI-UZAAGFTCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth B],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.744α = 90
b = 71.744β = 90
c = 126.36γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description