1LT6

HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYLGALACTOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin.

Merritt, E.A.Sarfaty, S.Feil, I.K.Hol, W.G.

(1997) Structure 5: 1485-1499

  • DOI: https://doi.org/10.1016/s0969-2126(97)00298-0
  • Primary Citation of Related Structures:  
    1LT5, 1LT6

  • PubMed Abstract: 

    Escherichia coli heat-labile enterotoxin (LT) is the causative agent of traveller's diarrhoea, and it is also responsible for the deaths of hundreds of thousands of children per year in developing countries. LT is highly homologous in sequence, structure and function to cholera toxin (CT). Both toxins attack intestinal epithelial cells via specific binding to the branched pentasaccharide of ganglioside GM1 at the cell surface. A receptor-binding antagonist which blocked this interaction would potentially constitute a prophylactic drug conferring protection both against the severe effects of cholera itself and against the milder but more common disease caused by LT. Four derivatives of the simple sugar galactose, members of a larger series of receptor antagonists identified by computer modeling and competitive binding studies, have been co-crystallized with either the full LT AB5 holotoxin or the LT B pentamer. These crystal structures have provided detailed views of the toxin in complex with each of the four antagonists: melibionic acid at 2.8 A resolution, lactulose at 2.65 A resolution, metanitrophenylgalactoside (MNPG) at 2.2 A resolution and thiodigalactoside (TDG) at 1.7 A resolution. The binding mode of each galactose derivative was observed 5-15 times, depending on the number of crystallographically independent toxin B pentamers per asymmetric unit. There is a remarkable consistency, with one important exception, in the location and hydrogen-bonding involvement of well-ordered water molecules at the receptor-binding site. The bound conformations of these receptor antagonist compounds preserve the toxin-galactose interactions previously observed for toxin-sugar complexes, but gain additional favorable interactions. The highest affinity compound, MNPG, is notable in that it displaces a water molecule that is observed to be well-ordered in all other previous and current crystal structures of toxin-sugar complexes. This could be a favorable entropic factor contributing to the increased affinity. The highest affinity members of the present set of antagonists (MNPG and TDG) bury roughly half (400 A2) of the binding-site surface covered by the full receptor GM1 pentasaccharide, despite being considerably smaller. This provides an encouraging basis for the creation of subsequent generations of derived compounds that can compete effectively with the natural receptor.


  • Organizational Affiliation

    Department of Biological Structure University of Washington Seattle, WA 98195-7742, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXIN103Escherichia coliMutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAA
Query on GAA

Download Ideal Coordinates CCD File 
K [auth D]
L [auth E]
M [auth F]
N [auth G]
O [auth H]
K [auth D],
L [auth E],
M [auth F],
N [auth G],
O [auth H],
P [auth L],
Q [auth M],
R [auth N],
S [auth O],
T [auth P]
3-nitrophenyl alpha-D-galactopyranoside
C12 H15 N O8
VCCMGHVCRFMITI-IIRVCBMXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GAA PDBBind:  1LT6 IC50: 5.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.67α = 90
b = 95.36β = 100.77
c = 85.65γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
MACROdata reduction
AMoREphasing
X-PLORrefinement
XENGENdata reduction
MACROdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    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: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-09
    Changes: Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Data collection, Structure summary