5N5T

14-3-3 sigma in complex with TAZ pS89 peptide and fragment NV2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening.

Sijbesma, E.Skora, L.Leysen, S.Brunsveld, L.Koch, U.Nussbaumer, P.Jahnke, W.Ottmann, C.

(2017) Biochemistry 56: 3972-3982

  • DOI: 10.1021/acs.biochem.7b00153
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins typically interact with multiple binding partners, and often different parts of their surfaces are employed to establish these protein-protein interactions (PPIs). Members of the class of 14-3-3 adapter proteins bind to several hundred other ...

    Proteins typically interact with multiple binding partners, and often different parts of their surfaces are employed to establish these protein-protein interactions (PPIs). Members of the class of 14-3-3 adapter proteins bind to several hundred other proteins in the cell. Multiple small molecules for the modulation of 14-3-3 PPIs have been disclosed; however, they all target the conserved phosphopeptide binding channel, so that selectivity is difficult to achieve. Here we report on the discovery of two individual secondary binding sites that have been identified by combining nuclear magnetic resonance-based fragment screening and X-ray crystallography. The two pockets that these fragments occupy are part of at least three physiologically relevant and structurally characterized 14-3-3 PPI interfaces, including those with serotonin N-acetyltransferase and plant transcription factor FT. In addition, the high degree of conservation of the two sites implies their relevance for 14-3-3 PPIs. This first identification of secondary sites on 14-3-3 proteins bound by small molecule ligands might facilitate the development of new chemical tool compounds for more selective PPI modulation.


    Organizational Affiliation

    Department of Chemistry, University of Duisburg-Essen , Essen, Germany.,Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Lead Discovery Center GmbH , Otto-Hahn-Stra├če 15, 44227 Dortmund, Germany.,Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein sigma
A
236Homo sapiensMutation(s): 0 
Gene Names: SFN (HME1)
Find proteins for P31947 (Homo sapiens)
Go to Gene View: SFN
Go to UniProtKB:  P31947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TAZ pS89 peptide
P
8Homo sapiensMutation(s): 0 
Gene Names: WWTR1 (TAZ)
Find proteins for Q9GZV5 (Homo sapiens)
Go to Gene View: WWTR1
Go to UniProtKB:  Q9GZV5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
8OB
Query on 8OB

Download SDF File 
Download CCD File 
A
4-[3,5-bis(chloranyl)pyridin-2-yl]oxyphenol
C11 H7 Cl2 N O2
NWFAJOGQUGZVOS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
P
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.512α = 90.00
b = 112.273β = 90.00
c = 62.591γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection