1RF2

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174
  • R-Value Work: 0.132

Literature

Macromolecules
Sequence Display for 1RF2

Classification: TOXIN

Total Structure Weight: 67363.16

Macromolecule Entities
Molecule Chains Length Organism Details
cholera toxin B protein (CTB) D, E, F, G, H 103 Vibrio cholerae Gene Name(s): ctxB toxB VC_1456
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BV4
Query on BV4

D, E, F, G, H 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)- BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO- 3,4-DIOXO-CYCLOBUTENYL]-AMINO-PROPOXY-ETHOXY- ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2-AMINO- PROPANE
BV4 (Synonym)
C79 H123 N15 O32
BPHYTQORKHDHAH-OHNHNXIVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

H TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

H 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BV4 N/A in BindingDB
IC50: 17000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174
  • R-Value Work: 0.132
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 102.24 α = 90.00
b = 66.03 β = 105.80
c = 78.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-11-07
  • Released Date: 2004-10-26
  • Deposition author(s): Pickens, J.C., Mitchell, D.D., Liu, J., Tan, X., Zhang, Z., Verlinde, C.L., Hol, W.G., Fan, E.

Revision History

  • Version 1_0: 2004-10-26

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance