4DTF

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++

Structural Biology Knowledgebase: 4DTF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DTF

Classification: TOXIN

Total Structure Weight: 44773.83

Macromolecule Entities
Molecule Chains Length Organism Details
VgrG protein A 396 Vibrio cholerae Fragment: unp residues 716-1111

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

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.177
  • Space Group: P 43 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.39 α = 90.00
b = 128.39 β = 90.00
c = 76.58 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