3TYI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.399 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nchem.1342

  • 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 grow ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c iso-1
A, B
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3Y
Query on T3Y

Download SDF File 
Download CCD File 
A, B
25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid
5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol
C28 H24 O16 S4
JFYBCAFLVNKHHG-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.399 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.044α = 90.00
b = 55.317β = 90.00
c = 117.419γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-08-08
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary