5LYC

Cytochrome c in complex with phosphonato-calix[6]arene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein Dimerization on a Phosphonated Calix[6]arene Disc.

Rennie, M.L.Doolan, A.M.Raston, C.L.Crowley, P.B.

(2017) Angew. Chem. Int. Ed. Engl. 56: 5517-5521

  • DOI: 10.1002/anie.201701500

  • PubMed Abstract: 
  • Complex formation between cationic cytochrome c and the water-soluble, poly-anionic p-phosphonatocalix[6]arene (pclx6 ) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx6 that acts like glue to med ...

    Complex formation between cationic cytochrome c and the water-soluble, poly-anionic p-phosphonatocalix[6]arene (pclx6 ) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx6 that acts like glue to mediate a symmetric (C2 ) protein dimer. The calixarene disc has a diameter of about 1.5 nm and masks about 360 Å2 of protein surface. The key protein-calixarene contacts occur via two linchpin lysines, with additional contacts provided by a small hydrophobic patch. The protein-calixarene supramolecular assemblies were observed in solution by size-exclusion chromatography with multi-angle light scattering and NMR spectroscopy. Using isothermal titration calorimetry and NMR data, an apparent Kd in the low micromolar range was determined for the charge-rich protein-calixarene complex. In contrast to p-sulfonatocalix[4]arene, the larger pclx6 has a single, well-defined binding site that mediates the assembly of cytochrome c in solution.


    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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7AZ
Query on 7AZ

Download SDF File 
Download CCD File 
A, B
phosphonato-calix[6]arene
C42 H42 O24 P6
QYHXEDFDCVRPFA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.570α = 90.00
b = 54.570β = 90.00
c = 208.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release