4I9O

Crystal Structure of GACKIX L664C Tethered to 1-10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ordering a dynamic protein via a small-molecule stabilizer.

Wang, N.Majmudar, C.Y.Pomerantz, W.C.Gagnon, J.K.Sadowsky, J.D.Meagher, J.L.Johnson, T.K.Stuckey, J.A.Brooks, C.L.Wells, J.A.Mapp, A.K.

(2013) J.Am.Chem.Soc. 135: 3363-3366

  • DOI: 10.1021/ja3122334

  • PubMed Abstract: 
  • Like many coactivators, the GACKIX domain of the master coactivator CBP/p300 recognizes transcriptional activators of diverse sequence composition via dynamic binding surfaces. The conformational dynamics of GACKIX that underlie its function also ren ...

    Like many coactivators, the GACKIX domain of the master coactivator CBP/p300 recognizes transcriptional activators of diverse sequence composition via dynamic binding surfaces. The conformational dynamics of GACKIX that underlie its function also render it especially challenging for structural characterization. We have found that the ligand discovery strategy of Tethering is an effective method for identifying small-molecule fragments that stabilize the GACKIX domain, enabling for the first time the crystallographic characterization of this important motif. The 2.0 Å resolution structure of GACKIX complexed to a small molecule was further analyzed by molecular dynamics simulations, which revealed the importance of specific side-chain motions that remodel the activator binding site in order to accommodate binding partners of distinct sequence and size. More broadly, these results suggest that Tethering can be a powerful strategy for identifying small-molecule stabilizers of conformationally malleable proteins, thus facilitating their structural characterization and accelerating the discovery of small-molecule modulators.


    Organizational Affiliation

    Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CREB-binding protein
A
101Mus musculusMutation(s): 1 
Gene Names: Crebbp (Cbp)
EC: 2.3.1.48
Find proteins for P45481 (Mus musculus)
Go to UniProtKB:  P45481
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KI1
Query on KI1

Download SDF File 
Download CCD File 
A
1-{4-[4-chloro-3-(trifluoromethyl)phenyl]-4-hydroxypiperidin-1-yl}-3-sulfanylpropan-1-one
C15 H17 Cl F3 N O2 S
STKPEUISNQZVRV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KI1Kd: 1900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 48.330α = 90.00
b = 48.330β = 90.00
c = 85.464γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
MD2data collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
BUSTER-TNTrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description