› 6zod

X-ray diffraction
2.85Å resolution

Fusidic acid binding to the allosteric deep transmembrane domain binding pocket, TM7/TM8 groove, and TM1/TM2 groove of the fully induced AcrB T protomer

Released:
DOI: 10.2210/pdb6zod/pdb
PDB entry 6zod coloured by chain, front view.
PDB entry 6zod coloured by chain, side view.
PDB entry 6zod coloured by chain, top view.
Source organisms:
Primary publication:
Allosteric drug transport mechanism of multidrug transporter AcrB.
Tam HK, Foong WE, Oswald C, Herrmann A, Zeng H, Pos KM
Nat Commun 12 3889 (2021)
PMID: 34188038

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151961 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Multidrug efflux pump subunit AcrB Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1057 amino acids
Theoretical weight: 114.74 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P31224 (Residues: 1-1049; Coverage: 100%)
Gene names: JW0451, acrB, acrE, b0462
Sequence domains: AcrB/AcrD/AcrF family
DARPIN Chains: D, E
Molecule details ›
Chains: D, E
Length: 169 amino acids
Theoretical weight: 18.32 KDa
Source organism: synthetic construct
Expression system: Escherichia coli K-12

Ligands and Environments

11 bound ligands:
Ligand LMT 7 x LMT
Ligand EDO 15 x EDO
Ligand GOL 2 x GOL
Ligand D10 2 x D10
Ligand FUA 4 x FUA
Ligand PGE 1 x PGE
Ligand 8K6 1 x 8K6
Ligand SO4 5 x SO4
Ligand PTY 2 x PTY
Ligand D12 1 x D12
Ligand HEX 1 x HEX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 145.985Å b: 166.129Å c: 243.683Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli K-12

Quick links

Citations

7 review citations

Molecular mechanisms of antibiotic resistance revisited.
Darby et al. (2023)
6 more

2 mentions without citation

Update on the Discovery of Efflux Pump Inhibitors against Critical Priority Gram-Negative Bacteria.
Compagne et al. (2023)
1 more