5LZH

Cholera toxin classical B-pentamer in complex with inhibitor PC262


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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 of 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. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin B subunit
A, B, D
103Vibrio choleraeMutation(s): 0 
Gene Names: ctxBEN12_07055ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003ERS013207_03244
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cholera enterotoxin B subunit
C, E
103Vibrio choleraeMutation(s): 0 
Gene Names: ctxBEN12_07055ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003ERS013207_03244
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7BN
Query on 7BN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
I [auth C],
L [auth D],
N [auth E]
(2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[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-propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid
C24 H39 N5 O14
AWGVVHYVQYXEMI-QRSXIJLLSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
M [auth D]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MRD
Query on MRD

Download Ideal Coordinates CCD File 
H [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
O [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth C],
K [auth C],
P [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.736α = 90
b = 66.063β = 105.67
c = 76.389γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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 2.0: 2018-02-14
    Changes: Atomic model, Derived calculations, Non-polymer description
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description