3ZM9

The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Mechanism of Allosteric Coupling in Choline Kinase A1 Revealed by a Rationally Designed Inhibitor

Sahun-Roncero, M.Rubio-Ruiz, B.Saladino, G.Conejo-Garcia, A.Espinosa, A.Velazquez-Campoy, A.Gervasio, F.L.Entrena, A.Hurtado-Guerrero, R.

(2013) Angew.Chem.Int.Ed.Engl. 52: 4582

  • DOI: 10.1002/anie.201209660

  • PubMed Abstract: 
  • Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the ...

    Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.


    Organizational Affiliation

    Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D; Fundacion ARAID, Edificio Pignatelli 36, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLINE KINASE ALPHA
A, B
383Homo sapiensGene Names: CHKA (CHK, CKI)
EC: 2.7.1.32, 2.7.1.82
Find proteins for P35790 (Homo sapiens)
Go to Gene View: CHKA
Go to UniProtKB:  P35790
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QMQ
Query on QMQ

Download SDF File 
Download CCD File 
A, B
1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium
C30 H34 N7
NKYSQEHAAOKBTL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QMQKd: 38 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.746α = 90.00
b = 121.214β = 90.00
c = 131.861γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-13
    Type: Database references
  • Version 1.2: 2013-04-17
    Type: Refinement description
  • Version 1.3: 2013-05-01
    Type: Database references