6BPL | pdb_00006bpl

E. coli MsbA in complex with LPS and inhibitor G907


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.283 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.233 (Depositor) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

Literature

Structural basis for dual-mode inhibition of the ABC transporter MsbA.

Ho, H.Miu, A.Alexander, M.K.Garcia, N.K.Oh, A.Zilberleyb, I.Reichelt, M.Austin, C.D.Tam, C.Shriver, S.Hu, H.Labadie, S.S.Liang, J.Wang, L.Wang, J.Lu, Y.Purkey, H.E.Quinn, J.Franke, Y.Clark, K.Beresini, M.H.Tan, M.W.Sellers, B.D.Maurer, T.Koehler, M.F.T.Wecksler, A.T.Kiefer, J.R.Verma, V.Xu, Y.Nishiyama, M.Payandeh, J.Koth, C.M.

(2018) Nature 557: 196-201

  • DOI: https://doi.org/10.1038/s41586-018-0083-5
  • Primary Citation Related Structures: 
    6BPL, 6BPP

  • PubMed Abstract: 

    The movement of core-lipopolysaccharide across the inner membrane of Gram-negative bacteria is catalysed by an essential ATP-binding cassette transporter, MsbA. Recent structures of MsbA and related transporters have provided insights into the molecular basis of active lipid transport; however, structural information about their pharmacological modulation remains limited. Here we report the 2.9 Å resolution structure of MsbA in complex with G907, a selective small-molecule antagonist with bactericidal activity, revealing an unprecedented mechanism of ABC transporter inhibition. G907 traps MsbA in an inward-facing, lipopolysaccharide-bound conformation by wedging into an architecturally conserved transmembrane pocket. A second allosteric mechanism of antagonism occurs through structural and functional uncoupling of the nucleotide-binding domains. This study establishes a framework for the selective modulation of ABC transporters and provides rational avenues for the design of new antibiotics and other therapeutics targeting this protein family.


  • Organizational Affiliation
    • Structural Biology, Genentech Inc., San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 136.48 kDa 
  • Atom Count: 9,180 
  • Modeled Residue Count: 1,141 
  • Deposited Residue Count: 1,164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipid A export ATP-binding/permease protein MsbA
A, B
582Escherichia coli CFT073Mutation(s): 0 
Gene Names: msbAc1054
EC: 3.6.3 (PDB Primary Data), 7.5.2.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8FJB1 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore Q8FJB1 
Go to UniProtKB:  Q8FJB1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8FJB1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose
C
5N/A
Glycosylation Resources
GlyTouCan: G00247JU
GlyCosmos: G00247JU
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose
D
4N/A
Glycosylation Resources
GlyTouCan: G68945FV
GlyCosmos: G68945FV

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
M [auth B],
N [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
AU7

Query on AU7



Download:Ideal Coordinates CCD File
F [auth A],
O [auth B]
(2E)-3-{6-[(1S)-1-(2-chloro-6-cyclopropylphenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid
C26 H24 Cl N O3
HOMQCLNBKVHZGD-RZXPCSSPSA-N
FTT

Query on FTT



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
R [auth B]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
MYR

Query on MYR



Download:Ideal Coordinates CCD File
J [auth A]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO

Query on DAO



Download:Ideal Coordinates CCD File
S [auth B]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
PA1

Query on PA1



Download:Ideal Coordinates CCD File
P [auth B]2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
DPO

Query on DPO



Download:Ideal Coordinates CCD File
T [auth B]DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
PO4

Query on PO4



Download:Ideal Coordinates CCD File
K [auth A],
Q [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.283 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.233 (Depositor) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.747α = 90
b = 91.606β = 89.39
c = 111.013γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.3: 2018-09-12
    Changes: Data collection, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary