MexB in complex with LMNG

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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This is version 1.2 of the entry. See complete history


Crystal structures of multidrug efflux pump MexB bound with high-molecular-mass compounds.

Sakurai, K.Yamasaki, S.Nakao, K.Nishino, K.Yamaguchi, A.Nakashima, R.

(2019) Sci Rep 9: 4359-4359

  • DOI: https://doi.org/10.1038/s41598-019-40232-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    RND-type multidrug efflux pumps have two voluminous multisite drug-binding pockets named the proximal and distal binding pocket. High- and low-molecular-mass drugs bind to these proximal and distal pocket, respectively. Here, we report the crystal structures of MexB of Pseudomonas aeruginosa bound with high-molecular-mass compounds. Contrary to the expectations, lauryl maltose neopentyl glycol (LMNG, MW 1,005), which is a surfactant larger than the proximal pocket-binding drugs, was found to bind to the distal pocket: one of the two hydrophobic alkyl chains was inserted into the hydrophobic pit, which is the binding site of the efflux pump inhibitor ABI-PP. LMNG is a substrate of the MexAB-OprM system and competitively inhibits the export of other substrates by this system. However, LMNG does not inhibit the export of other substrates by the inhibitor-binding-pit mutant F178W, which retains the export activity of LMNG. The crystal structure of this mutant suggested that the alkyl chain of LMNG could no longer be inserted into the pit because of steric hindrance. We also determined the crystal structure of MexB containing the high-molecular-mass compound neopentyl glycol derivative C7NG (MW 1,028), the binding site of which overlapped with LMNG in the distal pocket, indicating that whether a substrate binds to the distal or proximal pockets is controlled not only by its molecular weight but also by its individual molecular characteristic.

  • Organizational Affiliation

    Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug resistance protein MexB
A, B, C, D, E
A, B, C, D, E, F
1,052Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: mexBPA0426
Membrane Entity: Yes 
Find proteins for P52002 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P52002 
Go to UniProtKB:  P52002
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52002
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AV0

Download Ideal Coordinates CCD File 
G [auth B],
H [auth E]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
Experimental Data & Validation

Experimental Data

  • Resolution: 2.91 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.949α = 87.53
b = 134.343β = 70.2
c = 149.692γ = 89.02
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR12M6

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-12-13
    Changes: Derived calculations, Structure summary