1OY8

Structural Basis of Multiple Drug Binding Capacity of the AcrB Multidrug Efflux Pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump.

Yu, E.W.McDermott, G.Zgurskaya, H.I.Nikaido, H.Koshland, D.E.

(2003) Science 300: 976-980

  • DOI: 10.1126/science.1083137
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures ...

    Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acriflavine resistance protein B
A
1049Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrB (acrE)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Multi-Drug Efflux Transporters
Protein: 
AcrB bacterial multi-drug efflux transporter
Find proteins for P31224 (Escherichia coli (strain K12))
Go to UniProtKB:  P31224
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHQ
Query on RHQ

Download SDF File 
Download CCD File 
A
RHODAMINE 6G
C28 H31 N2 O3
IWWWBRIIGAXLCJ-KRUMMXJUSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.245 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 144.800α = 90.00
b = 144.800β = 90.00
c = 518.614γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance