6IDE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of theVibrio choleraeVqmA-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.

(2019) J. Biol. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator LuxR family
A, B
256Vibrio choleraeMutation(s): 0 
Find proteins for A0A0H6WEL7 (Vibrio cholerae)
Go to UniProtKB:  A0A0H6WEL7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3')C18Vibrio cholerae
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3')D18Vibrio cholerae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A1U
Query on A1U

Download SDF File 
Download CCD File 
A, B
3,5-dimethylpyrazin-2-ol
C6 H8 N2 O
AJYKJVCIKQEVCF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.780α = 90.00
b = 108.980β = 90.00
c = 214.320γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
xia2data reduction
CRANK2phasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570740
National Natural Science Foundation of ChinaChina81330076

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release