4DTH

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mg++

Structural Biology Knowledgebase: 4DTH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DTH

Classification: TOXIN

Total Structure Weight: 44870.88

Macromolecule Entities
Molecule Chains Length Organism Details
VgrG protein A 396 Vibrio cholerae Fragment: unp residues 716-1111
Gene Name(s): vgrG1 vgrG-1 VC0395_A1026

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.181
  • Space Group: P 43 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.68 α = 90.00
b = 128.68 β = 90.00
c = 76.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-21
  • Released Date: 2012-08-29
  • Deposition author(s): Durand, E., Audoly, G., Derrez, E., Spinelli, S., Ortiz-Lombardia, M., Cascales, E., Raoult, D., Cambillau, C.

Revision History

No revisions since initial release