6SUV | pdb_00006suv

Horse cytochrome c complexed by octa-anionic calixarene

PDB DOI: https://doi.org/10.2210/pdb6SUV/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Equus caballus
Expression System: Equus caballus
Mutation(s): No

Deposited: 2019-09-16 Released: 2020-07-22
Deposition Author(s): Geremia, S., Brancatelli, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.237 (Depositor), 0.204 (DCC)
R-Value Work:
0.170 (Depositor), 0.147 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene

Alex, J.M., Brancatelli, G., Volpi, S., Bonaccorso, C., Casnati, A., Geremia, S., Crowley, P.B.

(2020) Org Biomol Chem 18: 211-214

DOI: https://doi.org/10.1039/C9OB02275A

Macromolecule Content

Total Structure Weight: 108.1 kDa
Atom Count: 7,976
Modeled Residue Count: 832
Deposited Residue Count: 832
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A [auth AaA] B [auth BaB] C [auth CaC] D [auth DaD] E [auth EaE] A [auth AaA], B [auth BaB], C [auth CaC], D [auth DaD], E [auth EaE], F [auth FaF], G [auth GaG], H [auth HaH]	104	Equus caballus	Mutation(s): 0 Gene Names: CYCS, CYC
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004 Go to UniProtKB: P00004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6M7 (Subject of Investigation/LOI) Query on 6M7 Download:Ideal Coordinates CCD File SDF format, chain IA [auth GaG] SDF format, chain S [auth CaC] SDF format, chain W [auth DaD] SDF format, chain O [auth BaB] SDF format, chain MA [auth HaH] SDF format, chain K [auth AaA] SDF format, chain EA [auth FaF] SDF format, chain AA [auth EaE] MOL2 format, chain IA [auth GaG] MOL2 format, chain S [auth CaC] MOL2 format, chain W [auth DaD] MOL2 format, chain O [auth BaB] MOL2 format, chain MA [auth HaH] MOL2 format, chain K [auth AaA] MOL2 format, chain EA [auth FaF] MOL2 format, chain AA [auth EaE] mmCIF format, chain IA [auth GaG] mmCIF format, chain S [auth CaC] mmCIF format, chain W [auth DaD] mmCIF format, chain O [auth BaB] mmCIF format, chain MA [auth HaH] mmCIF format, chain K [auth AaA] mmCIF format, chain EA [auth FaF] mmCIF format, chain AA [auth EaE]	AA [auth EaE] EA [auth FaF] IA [auth GaG] K [auth AaA] MA [auth HaH] AA [auth EaE], EA [auth FaF], IA [auth GaG], K [auth AaA], MA [auth HaH], O [auth BaB], S [auth CaC], W [auth DaD]	octa-anionic calixarene C₃₈ H₃₉ As O₂₅ S₄ VEMYWEPWJISLAX-UHFFFAOYSA-N		Interactions Focus chain AA [auth EaE] Focus chain EA [auth FaF] Focus chain IA [auth GaG] Focus chain K [auth AaA] Focus chain MA [auth HaH] Focus chain O [auth BaB] Focus chain S [auth CaC] Focus chain W [auth DaD] Interactions & Density Focus chain AA [auth EaE] Focus chain EA [auth FaF] Focus chain IA [auth GaG] Focus chain K [auth AaA] Focus chain MA [auth HaH] Focus chain O [auth BaB] Focus chain S [auth CaC] Focus chain W [auth DaD]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain Z [auth EaE] SDF format, chain V [auth DaD] SDF format, chain R [auth CaC] SDF format, chain N [auth BaB] SDF format, chain LA [auth HaH] SDF format, chain J [auth AaA] SDF format, chain HA [auth GaG] SDF format, chain DA [auth FaF] MOL2 format, chain Z [auth EaE] MOL2 format, chain V [auth DaD] MOL2 format, chain R [auth CaC] MOL2 format, chain N [auth BaB] MOL2 format, chain LA [auth HaH] MOL2 format, chain J [auth AaA] MOL2 format, chain HA [auth GaG] MOL2 format, chain DA [auth FaF] mmCIF format, chain Z [auth EaE] mmCIF format, chain V [auth DaD] mmCIF format, chain R [auth CaC] mmCIF format, chain N [auth BaB] mmCIF format, chain LA [auth HaH] mmCIF format, chain J [auth AaA] mmCIF format, chain HA [auth GaG] mmCIF format, chain DA [auth FaF]	DA [auth FaF] HA [auth GaG] J [auth AaA] LA [auth HaH] N [auth BaB] DA [auth FaF], HA [auth GaG], J [auth AaA], LA [auth HaH], N [auth BaB], R [auth CaC], V [auth DaD], Z [auth EaE]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain DA [auth FaF] Focus chain HA [auth GaG] Focus chain J [auth AaA] Focus chain LA [auth HaH] Focus chain N [auth BaB] Focus chain R [auth CaC] Focus chain V [auth DaD] Focus chain Z [auth EaE] Interactions & Density Focus chain DA [auth FaF] Focus chain HA [auth GaG] Focus chain J [auth AaA] Focus chain LA [auth HaH] Focus chain N [auth BaB] Focus chain R [auth CaC] Focus chain V [auth DaD] Focus chain Z [auth EaE]
ACE Query on ACE Download:Ideal Coordinates CCD File SDF format, chain GA [auth GaG] SDF format, chain I [auth AaA] SDF format, chain KA [auth HaH] SDF format, chain M [auth BaB] SDF format, chain Q [auth CaC] SDF format, chain U [auth DaD] SDF format, chain Y [auth EaE] SDF format, chain CA [auth FaF] MOL2 format, chain GA [auth GaG] MOL2 format, chain I [auth AaA] MOL2 format, chain KA [auth HaH] MOL2 format, chain M [auth BaB] MOL2 format, chain Q [auth CaC] MOL2 format, chain U [auth DaD] MOL2 format, chain Y [auth EaE] MOL2 format, chain CA [auth FaF] mmCIF format, chain GA [auth GaG] mmCIF format, chain I [auth AaA] mmCIF format, chain KA [auth HaH] mmCIF format, chain M [auth BaB] mmCIF format, chain Q [auth CaC] mmCIF format, chain U [auth DaD] mmCIF format, chain Y [auth EaE] mmCIF format, chain CA [auth FaF]	CA [auth FaF] GA [auth GaG] I [auth AaA] KA [auth HaH] M [auth BaB] CA [auth FaF], GA [auth GaG], I [auth AaA], KA [auth HaH], M [auth BaB], Q [auth CaC], U [auth DaD], Y [auth EaE]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain CA [auth FaF] Focus chain GA [auth GaG] Focus chain I [auth AaA] Focus chain KA [auth HaH] Focus chain M [auth BaB] Focus chain Q [auth CaC] Focus chain U [auth DaD] Focus chain Y [auth EaE] Interactions & Density Focus chain CA [auth FaF] Focus chain GA [auth GaG] Focus chain I [auth AaA] Focus chain KA [auth HaH] Focus chain M [auth BaB] Focus chain Q [auth CaC] Focus chain U [auth DaD] Focus chain Y [auth EaE]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain X [auth DaD] SDF format, chain T [auth CaC] SDF format, chain P [auth BaB] SDF format, chain NA [auth HaH] SDF format, chain L [auth AaA] SDF format, chain JA [auth GaG] SDF format, chain FA [auth FaF] SDF format, chain BA [auth EaE] MOL2 format, chain X [auth DaD] MOL2 format, chain T [auth CaC] MOL2 format, chain P [auth BaB] MOL2 format, chain NA [auth HaH] MOL2 format, chain L [auth AaA] MOL2 format, chain JA [auth GaG] MOL2 format, chain FA [auth FaF] MOL2 format, chain BA [auth EaE] mmCIF format, chain X [auth DaD] mmCIF format, chain T [auth CaC] mmCIF format, chain P [auth BaB] mmCIF format, chain NA [auth HaH] mmCIF format, chain L [auth AaA] mmCIF format, chain JA [auth GaG] mmCIF format, chain FA [auth FaF] mmCIF format, chain BA [auth EaE]	BA [auth EaE] FA [auth FaF] JA [auth GaG] L [auth AaA] NA [auth HaH] BA [auth EaE], FA [auth FaF], JA [auth GaG], L [auth AaA], NA [auth HaH], P [auth BaB], T [auth CaC], X [auth DaD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth EaE] Focus chain FA [auth FaF] Focus chain JA [auth GaG] Focus chain L [auth AaA] Focus chain NA [auth HaH] Focus chain P [auth BaB] Focus chain T [auth CaC] Focus chain X [auth DaD] Interactions & Density Focus chain BA [auth EaE] Focus chain FA [auth FaF] Focus chain JA [auth GaG] Focus chain L [auth AaA] Focus chain NA [auth HaH] Focus chain P [auth BaB] Focus chain T [auth CaC] Focus chain X [auth DaD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237 (Depositor), 0.204 (DCC)
R-Value Work: 0.170 (Depositor), 0.147 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.591	α = 90
b = 65.591	β = 90
c = 250.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

Geremia, S.

Brancatelli, G.

Revision History (Full details and data files)

Version 1.0: 2020-07-22
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 2.0: 2026-09-02
Type: Remediation
Reason: Metalloprotein remediation
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary