5KPF

Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex

• PDB DOI: https://doi.org/10.2210/pdb5KPF/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-04 Released: 2017-07-12 
• Deposition Author(s): Doolan, A.M., Rennie, M.L., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Protein Recognition by Functionalized Sulfonatocalix[4]arenes.

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

(2018) Chemistry 24: 984-991

• PubMed: 29125201 
• DOI: https://doi.org/10.1002/chem.201704931
• Primary Citation of Related Structures:  
  5KPF, 5LFT, 5T8W


• PubMed Abstract: 
  

  The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.12 kDa 
• Atom Count: 2,120 
• Modelled Residue Count: 216 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A, B	108	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6VJ	F [auth B]	Phenyl-trisulfonatocalix[4]arene C34 H28 O13 S3 YFNBDSGSCMLGRM-UHFFFAOYSA-N
HEC	C [auth A], E [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.417	α = 90
b = 61.085	β = 90
c = 173.403	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Doolan, A.M., Rennie, M.L., Crowley, P.B.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/ERC/B2912

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2018-02-28
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary