4E1C

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

Structural Biology Knowledgebase: 4E1C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 4E1C

Classification: TOXIN

Total Structure Weight: 44694.81

Macromolecule Entities
Molecule Chains Length Organism Details
VgrG protein A 396 Vibrio cholerae EC#: 6.3.2 IUBMB
Fragment: Vibrio cholerae VgrG1 ACD (unp residues 716-1111)
Gene Name(s): vgrG1 vgrG-1 VC0395_A1026
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.174
  • Space Group: P 43 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.46 α = 90.00
b = 128.46 β = 90.00
c = 76.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-06
  • 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