1LLR

CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0012


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Characterization and crystal structure of a high-affinity pentavalent receptor-binding inhibitor for cholera toxin and E. coli heat-labile enterotoxin.

Merritt, E.A.Zhang, Z.Pickens, J.C.Ahn, M.Hol, W.G.Fan, E.

(2002) J Am Chem Soc 124: 8818-8824

  • DOI: https://doi.org/10.1021/ja0202560
  • Primary Citation of Related Structures:  
    1LLR

  • PubMed Abstract: 

    Multivalent ligand design constitutes an attractive avenue to the inhibition of receptor recognition and other biological events mediated by oligomeric proteins with multiple binding sites. One example is the design of multivalent receptor blockers targeting members of the AB(5) bacterial toxin family. We report here the synthesis and characterization of a pentavalent inhibitor for cholera toxin and Escherichia coli heat-labile enterotoxin. This inhibitor is an advance over the symmetric pentacyclen-derived inhibitor described in our earlier work in that it presents five copies of m-nitrophenyl-alpha-D-galactoside (MNPG) rather than five copies of beta-D-galactose. The approximately 100-fold higher single-site affinity of MNPG for the toxin receptor binding site relative to galactose is found to yield a proportionate increase in the affinity and IC50 measured for the respective pentavalent constructs. We show by dynamic light scattering that inhibition of receptor binding by the pentavalent inhibitor is due to 1:1 inhibitor:toxin association rather than to inhibitor-mediated aggregation. This 1:1 association is in complete agreement with a 1.46 A resolution crystal structure of the pentavalent inhibitor:toxin complex, which shows that the favorable single-site binding interactions of MNPG are retained by the five arms of the 5256 Da pentavalent MNPG-based inhibitor and that the initial segment of the linking groups interacts with the surface of the toxin B pentamer.


  • Organizational Affiliation

    Department of Biochemistry and Biological Structure, University of Washington, Box 357742, Seattle, Washington 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLERA TOXIN B SUBUNITA [auth D],
B [auth E],
C [auth F],
D [auth G],
E [auth H]
103Vibrio choleraeMutation(s): 0 
Gene Names: CTXB
UniProt
Find proteins for Q57193 (Vibrio cholerae)
Explore Q57193 
Go to UniProtKB:  Q57193
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57193
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FNG
Query on FNG

Download Ideal Coordinates CCD File 
F [auth D],
H [auth E],
J [auth F],
L [auth G],
N [auth H]
5-aminocarbonyl-3-nitrophenyl alpha-D-galactopyranoside
C13 H16 N2 O9
BYSXBFJVGIOFBO-LNSPPBFMSA-N
LNQ
Query on LNQ

Download Ideal Coordinates CCD File 
G [auth D],
I [auth E],
K [auth F],
M [auth G],
O [auth H]
3-AMINO-4-{3-[2-(2-PROPOXY-ETHOXY)-ETHOXY]-PROPYLAMINO}-CYCLOBUT-3-ENE-1,2-DIONE
C14 H24 N2 O5
ZUVPNXOKAPTNLU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.391α = 90
b = 65.964β = 105.97
c = 78.146γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary