4DX5

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

Structural Biology Knowledgebase: 4DX5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 4DX5

Classification: MEMBRANE PROTEIN TRANSPORT PROTEIN

Total Structure Weight: 390625.88

Macromolecule Entities
Molecule Chains Length Organism Details
Acriflavine resistance protein B A, B, C 1057 Escherichia coli Gene Name(s): acrB acrE b0462 JW0451
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DARPIN D, E 169 Synthetic construct

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Multi-Drug Efflux Transporters

Protein Name: AcrB bacterial multi-drug efflux transporter


Small Molecules
Ligands 12 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LMT
Query on LMT

A, B, C DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMU
Query on LMU

B DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MIY
Query on MIY

B (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)- 3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A- OCTAHYDROTETRACENE-2-CARBOXAMIDE
MINOCYCLINE (Synonym)
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
C14
Query on C14

B TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D12
Query on D12

A, B, C DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UND
Query on UND

C UNDECANE
LIPID FRAGMENT (Synonym)
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D10
Query on D10

A, B, C DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DD9
Query on DD9

C nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OCT
Query on OCT

A, C N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEX
Query on HEX

A, B, C HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.200
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 145.99 α = 90.00
b = 161.72 β = 90.00
c = 245.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-27
  • Released Date: 2012-05-02
  • Deposition author(s): Eicher, T., Cha, H., Seeger, M.A., Brandstaetter, L., El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Gruetter, M.G., Diederichs, K., Pos, K.M.

Revision History

  • 2014-01-29
    Type: Source and taxonomy | Details: --