6Q4P

Fusidic acid bound AcrB_N298A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.

Tam, H.K.Malviya, V.N.Foong, W.E.Herrmann, A.Malloci, G.Ruggerone, P.Vargiu, A.V.Pos, K.M.

(2020) J Mol Biol 432: 861-877

  • DOI: https://doi.org/10.1016/j.jmb.2019.12.025
  • Primary Citation of Related Structures:  
    6Q4N, 6Q4O, 6Q4P

  • PubMed Abstract: 

    AcrAB(Z)-TolC is the main drug efflux transporter complex in Escherichia coli. The extrusion of various toxic compounds depends on several drug binding sites within the trimeric AcrB transporter. Membrane-localized carboxylated substrates, such as fusidic acid and hydrophobic β-lactams, access the pump via a groove between the transmembrane helices TM1 and TM2. In this article, the transport route from the initial TM1/TM2 groove binding site toward the deep binding pocket located in the periplasmic part has been addressed via molecular modeling studies followed by functional and structural characterization of several AcrB variants. We propose that membrane-embedded drugs bind initially to the TM1/TM2 groove, are oriented by the AcrB PN2 subdomain, and are subsequently transported via a PN2/PC1 interface pathway directly toward the deep binding pocket. Our work emphasizes the exploitation of multiple transport pathways by AcrB tuned to substrate physicochemical properties related to the polyspecificity of the pump.


  • Organizational Affiliation

    Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB
A, B, C
1,057Escherichia coli K-12Mutation(s): 1 
Gene Names: acrBacrEb0462JW0451
Membrane Entity: Yes 
UniProt
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DARPin
D, E
169synthetic constructMutation(s): 0 
Gene Names: Artificial gene
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY
Query on PTY

Download Ideal Coordinates CCD File 
IA [auth C],
T [auth B]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
FUA
Query on FUA

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S [auth B]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
LMT
Query on LMT

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F [auth A]
FA [auth C]
G [auth A]
GA [auth C]
H [auth A]
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
P [auth B],
Q [auth B],
R [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
DDR
Query on DDR

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V [auth B](2S)-3-hydroxypropane-1,2-diyl didecanoate
C23 H44 O5
GNSDEDOVXZDMKM-NRFANRHFSA-N
ETE
Query on ETE

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UA [auth C]2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
DDQ
Query on DDQ

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K [auth A]
LA [auth C]
MA [auth C]
NA [auth C]
W [auth B]
K [auth A],
LA [auth C],
MA [auth C],
NA [auth C],
W [auth B],
X [auth B]
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
C14
Query on C14

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KA [auth C]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12
Query on D12

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J [auth A],
JA [auth C],
U [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
Query on D10

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EA [auth B]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

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OA [auth C],
Y [auth B],
Z [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
SO4
Query on SO4

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BA [auth B],
CA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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DA [auth B]
L [auth A]
M [auth A]
N [auth A]
TA [auth C]
DA [auth B],
L [auth A],
M [auth A],
N [auth A],
TA [auth C],
WA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEX
Query on HEX

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O [auth A],
VA [auth C]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
CL
Query on CL

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AA [auth B],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.222α = 90
b = 162.632β = 90
c = 245.467γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB807 (Transport and Communication across Biological Membranes
German Research FoundationGermanyDFG EXC115 (Cluster of Excellence Frankfurt Macromolecular Complexes)

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description