› 6ide

X-ray diffraction
2.51Å resolution

Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design

Released:
DOI: 10.2210/pdb6ide/pdb
PDB entry 6ide coloured by chain, front view.
PDB entry 6ide coloured by chain, side view.
PDB entry 6ide coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
Crystal structure of the Vibrio cholerae VqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design.
Wu H, Li M, Guo H, Zhou H, Li B, Xu Q, Xu C, Yu F, He J
J Biol Chem 294 2580-2592 (2019)
PMID: 30610119

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-120008 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional regulator LuxR family Chains: A, B
Molecule details ›
Chains: A, B
Length: 256 amino acids
Theoretical weight: 28.87 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
Source organism: Vibrio cholerae
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: Vibrio cholerae
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand A1U 2 x A1U
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 52.78Å b: 108.98Å c: 214.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Interface of Vibrio cholerae and the Gut Microbiome.
Cho et al. (2021)
4 other articles

5 mentions without citation

PAS domains in bacterial signal transduction.
Stuffle et al. (2021)
4 more