3TYI

Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T3YClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Protein camouflage in cytochrome c-calixarene complexes.

McGovern, R.E.Fernandes, H.Khan, A.R.Power, N.P.Crowley, P.B.

(2012) Nat Chem 4: 527-533

  • DOI: https://doi.org/10.1038/nchem.1342
  • Primary Citation of Related Structures:  
    3TYI

  • PubMed Abstract: 

    Small molecules that recognize protein surfaces are important tools for modifying protein interaction properties. Since the 1980s, several thousand studies concerning calixarenes and host-guest interactions have been published. Although there is growing interest in protein-calixarene interactions, only limited structural information has been available to date. We now report the crystal structure of a protein-calixarene complex. The water-soluble p-sulfonatocalix[4]arene is shown to bind the lysine-rich cytochrome c at three different sites. Binding curves obtained from NMR titrations reveal an interaction process that involves two or more binding sites. Together, the data indicate a dynamic complex in which the calixarene explores the surface of cytochrome c. In addition to providing valuable information on protein recognition, the data also indicate that the calixarene is a mediator of protein-protein interactions, with potential applications in generating assemblies and promoting crystallization.


  • Organizational Affiliation

    School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
A, B
108Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: CYC1YJR048WJ1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.044α = 90
b = 55.317β = 90
c = 117.419γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T3YClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description