5LZI | pdb_00005lzi

Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.176 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.148 (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 1.3 of the entry. See complete history

Literature

Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics.

Heggelund, J.E.Mackenzie, A.Martinsen, T.Benjamin Heim, J.Cheshev, P.Bernardi, A.Krengel, U.

(2017) Sci Rep 7: 2326-2326

  • DOI: https://doi.org/10.1038/s41598-017-02179-0
  • Primary Citation Related Structures: 
    5LZG, 5LZH, 5LZI, 5LZJ

  • PubMed Abstract: 

    Cholera is a life-threatening disease in many countries, and new drugs are clearly needed. C-glycosidic antagonists may serve such a purpose. Here we report atomic-resolution crystal structures of three such compounds in complexes with the cholera toxin. The structures give unprecedented atomic details of the molecular interactions and show how the inhibitors efficiently block the GM1 binding site. These molecules are well suited for development into low-cost prophylactic drugs, due to their relatively easy synthesis and their resistance to glycolytic enzymes. One of the compounds links two toxin B-pentamers in the crystal structure, which may yield improved inhibition through the formation of toxin aggregates. These structures can spark the improved design of GM1 mimics, either alone or as multivalent inhibitors connecting multiple GM1-binding sites. Future developments may further include compounds that link the primary and secondary binding sites. Serving as decoys, receptor mimics may lessen symptoms while avoiding the use of antibiotics.


  • Organizational Affiliation
    • Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway. j.e.heggelund@farmasi.uio.no.

Macromolecule Content 

  • Total Structure Weight: 63.38 kDa 
  • Atom Count: 5,453 
  • 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
Heat-labile enterotoxin B chain
A, B, C, D, E
103Escherichia coliMutation(s): 1 
Gene Names: eltBltpB
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7DB

Query on 7DB



Download:Ideal Coordinates CCD File
K [auth B],
M [auth C],
P [auth D],
Q [auth E]
(2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{S})-3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-2-(2-phenylethanoylamino)propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid
C32 H46 N6 O15
VJJPXKHAIAQVCK-WZAWTCGUSA-N
7BQ

Query on 7BQ



Download:Ideal Coordinates CCD File
G [auth A](2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{R})-3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-2-(2-phenylethanoylamino)propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid
C32 H46 N6 O15
VJJPXKHAIAQVCK-WOQXIOLNSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
N [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
J [auth B],
L [auth C],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.176 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.17α = 90
b = 75.87β = 90
c = 125.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary