8R3C

Cocrystal form II of the Pent - sulfonato-calix[8]arene complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Multivalent Calixarene Complexation of a Designed Pentameric Lectin.

Flood, R.J.Cerofolini, L.Fragai, M.Crowley, P.B.

(2024) Biomacromolecules 25: 1303-1309

  • DOI: https://doi.org/10.1021/acs.biomac.3c01280
  • Primary Citation of Related Structures:  
    8R3B, 8R3C, 8R3D

  • PubMed Abstract: 

    We describe complex formation between a designed pentameric β-propeller and the anionic macrocycle sulfonato-calix[8]arene ( sclx 8 ), as characterized by X-ray crystallography and NMR spectroscopy. Two crystal structures and 15 N HSQC experiments reveal a single calixarene binding site in the concave pocket of the β-propeller toroid. Despite the symmetry mismatch between the pentameric protein and the octameric macrocycle, they form a high affinity multivalent complex, with the largest protein-calixarene interface observed to date. This system provides a platform for investigating multivalency.


  • Organizational Affiliation

    SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta propeller
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
48Enterobacteria phage L1Mutation(s): 1 
UniProt
Find proteins for A0A140UHM9 (Enterobacteria phage L1)
Explore A0A140UHM9 
Go to UniProtKB:  A0A140UHM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140UHM9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVB (Subject of Investigation/LOI)
Query on EVB

Download Ideal Coordinates CCD File 
P [auth E]sulfonato-calix[8]arene
C56 H48 O32 S8
KCEGJGDGMRAJEP-UHFFFAOYSA-N
NDG
Query on NDG

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth B]
N [auth D]
O [auth D]
K [auth A],
L [auth A],
M [auth B],
N [auth D],
O [auth D],
Q [auth F],
R [auth G],
S [auth H],
T [auth H],
U [auth I]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.975α = 90
b = 52.055β = 104.37
c = 69.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/RC/2275_P2

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release