8R3C | pdb_00008r3c

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

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
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
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  • 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]
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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EVBClick on this verticalbar to view details

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