6Y0J

Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Protein-macrocycle framework engineering: supramolecular copolymerisation with two disparate calixarenes

Mockler, N.M.Engilberge, S.Rennie, M.L.Raston, C.L.Crowley, P.B.

(2021) Supramolecular Chemistry : 1-7


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
A, B, C, D
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVB (Subject of Investigation/LOI)
Query on EVB

Download Ideal Coordinates CCD File 
I [auth B],
L [auth C]
sulfonato-calix[8]arene
C56 H48 O32 S8
KCEGJGDGMRAJEP-UHFFFAOYSA-N
7AZ (Subject of Investigation/LOI)
Query on 7AZ

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
K [auth C],
N [auth D]
phosphonato-calix[6]arene
C42 H42 O24 P6
QYHXEDFDCVRPFA-UHFFFAOYSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
J [auth C],
M [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.573α = 90
b = 67.573β = 90
c = 373.866γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description