1JR0 | pdb_00001jr0

CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.183 (Depositor) 
  • R-Value Work: 
    0.138 (DCC) 
  • R-Value Observed: 
    0.131 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes.

Pickens, J.C.Merritt, E.A.Ahn, M.Verlinde, C.L.Hol, W.G.Fan, E.

(2002) Chem Biol 9: 215-224

  • DOI: https://doi.org/10.1016/s1074-5521(02)00097-2
  • Primary Citation Related Structures: 
    1JQY, 1JR0

  • PubMed Abstract: 

    The action of cholera toxin and E. coli heat-labile enterotoxin can be inhibited by blocking their binding to the cell-surface receptor GM1. We have used anchor-based design to create 15 receptor binding inhibitors that contain the previously characterized inhibitor MNPG as a substructure. In ELISA assays, all 15 compounds exhibited increased potency relative to MNPG. Binding affinities for two compounds, each containing a morpholine ring linked to MNPG via a hydrophobic tail, were characterized by pulsed ultrafiltration (PUF) and isothermal titration calorimetry (ITC). Crystal structures for these compounds bound to toxin B pentamer revealed a conserved binding mode for the MNPG moiety, with multiple binding modes adopted by the attached morpholine derivatives. The observed binding interactions can be exploited in the design of improved toxin binding inhibitors.


  • Organizational Affiliation
    • Department of Biological Structure, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 60.4 kDa 
  • Atom Count: 5,015 
  • Modeled Residue Count: 515 
  • Deposited Residue Count: 515 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P01556 
Go to UniProtKB:  P01556
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01556
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.183 (Depositor) 
  • R-Value Work:  0.138 (DCC) 
  • R-Value Observed: 0.131 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.098α = 90
b = 66.064β = 105.74
c = 78.565γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary