6Y0J

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
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

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	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]