5OEH | pdb_00005oeh

Molecular tweezers modulate 14-3-3 protein-protein interactions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular tweezers modulate 14-3-3 protein-protein interactions.

Bier, D.Rose, R.Bravo-Rodriguez, K.Bartel, M.Ramirez-Anguita, J.M.Dutt, S.Wilch, C.Klarner, F.G.Sanchez-Garcia, E.Schrader, T.Ottmann, C.

(2013) Nat Chem 5: 234-239

  • DOI: https://doi.org/10.1038/nchem.1570
  • Primary Citation Related Structures: 
    5OEG, 5OEH

  • PubMed Abstract: 

    Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins--a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)--in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.


  • Organizational Affiliation
    • Chemical Genomics Centre of the Max-Planck-Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 27.4 kDa 
  • Atom Count: 1,918 
  • Modeled Residue Count: 230 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9SZ

Query on 9SZ



Download:Ideal Coordinates CCD File
B [auth A](1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene
C42 H32 O8 P2
BZESKQAEKFQSPD-FCODNRGNSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.4α = 90
b = 157.4β = 90
c = 77.2γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Derived calculations
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Refinement description