1JQY

HEAT-LABILE ENTEROTOXIN B-PENTAMER WITH LIGAND BMSC-0010


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.3 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXIN B CHAIN103Escherichia coliMutation(s): 0 
Gene Names: ETXB
UniProt
Find proteins for P32890 (Escherichia coli)
Explore P32890 
Go to UniProtKB:  P32890
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32890
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A32
Query on A32

Download Ideal Coordinates CCD File 
AA [auth X]
BA [auth Y]
CA [auth Z]
P [auth D]
Q [auth E]
AA [auth X],
BA [auth Y],
CA [auth Z],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth L],
V [auth M],
W [auth O],
X [auth P],
Y [auth V],
Z [auth W]
(3-NITRO-5-(3-MORPHOLIN-4-YL-PROPYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE
C20 H29 N3 O10
CBPMHEKCQNCVNT-QTVCLEQKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A32 Binding MOAD:  1JQY Ki: 1.20e+4 (nM) from 1 assay(s)
PDBBind:  1JQY Ki: 1.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.99α = 90
b = 166.006β = 92.13
c = 74.42γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



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: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description