1RD9

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.

Pickens, J.C.Mitchell, D.D.Liu, J.Tan, X.Zhang, Z.Verlinde, C.L.Hol, W.G.Fan, E.

(2004) Chem.Biol. 11: 1205-1215

  • DOI: 10.1016/j.chembiol.2004.06.008
  • Primary Citation of Related Structures:  1RCV, 1RDP, 1RF2

  • PubMed Abstract: 
  • A series of bivalent ligands of varying length were synthesized to inhibit the receptor-binding process of cholera toxin. Competitive surface receptor binding assays showed that significant potency gains relative to the constituent monovalent ligands ...

    A series of bivalent ligands of varying length were synthesized to inhibit the receptor-binding process of cholera toxin. Competitive surface receptor binding assays showed that significant potency gains relative to the constituent monovalent ligands were achieved independently from the ability of the extended bivalent ligands to span binding sites within the toxin pentamer. Several models that could account for the unexpected improvement in IC(50) values are examined, taking into account crystallographic analysis of each ligand in complex with the toxin pentamer. Evidence is presented that steric blocking at the receptor binding surface may play a role. The results of our study suggest that the use of relatively short, "nonspanning" bivalent ligands, or monovalent ligands of similar topology and bulk may be an effective way of blocking the interaction of multimeric proteins with their cell surface receptors.


    Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cholera toxin B protein (CTB)
D, E, F, G, H
103Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Gene Names: ctxB (toxB)
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  P01556
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BV2
Query on BV2

Download SDF File 
Download CCD File 
D, E, F, G, H
1,3-BIS-([3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYL-AMINO]-CARBONYLOXY)-2-AMINO-PROPANE
BV2
C51 H79 N11 O22
RJLCAAJYVGPDFG-LNGNCPBTSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
H
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
H
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BV2IC50: 13000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.131 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.983α = 90.00
b = 66.072β = 105.84
c = 77.818γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
XTALVIEWrefinement
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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