1RDP

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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:  
    1RD9, 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 were achieved independently from the ability of the extended bivalent ligands to span binding sites within the toxin pentamer ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cholera toxin B protein (CTB)A [auth D], B [auth E], C [auth F], D [auth G], E [auth H]103Vibrio choleraeMutation(s): 0 
Gene Names: ctxB
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BV3
Query on BV3

Download Ideal Coordinates CCD File 
F [auth D], G [auth E], H [auth F], I [auth G], J [auth H]1,3-BIS-([[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBU TENYL]-AMINO-ETHYL]-AMINO-CARBONYLOXY)-2-AMINO-PROPANE
C63 H91 N15 O26
HQTVCYHBYUXJDJ-ISUJOEFPSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
L [auth H]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
K [auth H]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BV3IC50:  9000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.09α = 90
b = 66.079β = 105.83
c = 78.715γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance