6Y0J | pdb_00006y0j

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

PDB DOI: https://doi.org/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 (Depositor), 0.270 (DCC)
R-Value Work:
0.245 (Depositor), 0.256 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

DOI: https://doi.org/10.1080/10610278.2021.1935946

Macromolecule Content

Total Structure Weight: 58.09 kDa
Atom Count: 4,094
Modeled Residue Count: 427
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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| 3D 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
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044 Go to UniProtKB: P00044
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00044
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.245 (Depositor), 0.256 (DCC)
R-Value Observed: 0.246 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Engilberge, S.

Rennie, M.L.

Crowley, P.B.

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/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
Version 1.3: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary

6Y0J | pdb_00006y0j

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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