Macromolecule Content

Total Structure Weight: 58.09 kDa
Atom Count: 4094
Residue Count: 427
Unique protein chains: 1

6Y0J

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

DOI: 10.2210/pdb6Y0J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-02-07 Released: 2021-02-17
Deposition Author(s): Engilberge, S., Rennie, M.L., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

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

wwPDB Validation 3D Report Full Report

Literature

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

Engilberge, S., Rennie, M.L., Crowley, P.B.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A, B, C, D	108	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: CYC1, YJR048W, J1653
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044 Go to UniProtKB: P00044
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EVB Query on EVB Download Ideal Coordinates CCD File SDF format, chain I [B] SDF format, chain L [C] MOL2 format, chain I [B] MOL2 format, chain L [C]	B, C	sulfonato-calix[8]arene C₅₆ H₄₈ O₃₂ S₈ KCEGJGDGMRAJEP-UHFFFAOYSA-N		Ligand Interaction
7AZ Query on 7AZ Download Ideal Coordinates CCD File SDF format, chain G [B] SDF format, chain H [B] SDF format, chain K [C] SDF format, chain N [D] MOL2 format, chain G [B] MOL2 format, chain H [B] MOL2 format, chain K [C] MOL2 format, chain N [D]	B, C, D	phosphonato-calix[6]arene C₄₂ H₄₂ O₂₄ P₆ QYHXEDFDCVRPFA-UHFFFAOYSA-N		Ligand Interaction
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [B] SDF format, chain J [C] SDF format, chain M [D] MOL2 format, chain E [A] MOL2 format, chain F [B] MOL2 format, chain J [C] MOL2 format, chain M [D]	A, B, C, D	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Ligand Interaction

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 = 67.573	α = 90
b = 67.573	β = 90
c = 373.866	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-02-07
Released Date: 2021-02-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/CDA/2168

Revision History

Version 1.0: 2021-02-17
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.