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 1.1 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: 108.06 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LVQ (Subject of Investigation/LOI) Query on LVQ Download:Ideal Coordinates CCD File SDF format, chain CA [auth GaG] SDF format, chain FA [auth HaH] SDF format, chain K [auth AaA] SDF format, chain N [auth BaB] SDF format, chain T [auth DaD] SDF format, chain W [auth EaE] SDF format, chain Z [auth FaF] SDF format, chain Q [auth CaC] MOL2 format, chain CA [auth GaG] MOL2 format, chain FA [auth HaH] MOL2 format, chain K [auth AaA] MOL2 format, chain N [auth BaB] MOL2 format, chain T [auth DaD] MOL2 format, chain W [auth EaE] MOL2 format, chain Z [auth FaF] MOL2 format, chain Q [auth CaC] mmCIF format, chain CA [auth GaG] mmCIF format, chain FA [auth HaH] mmCIF format, chain K [auth AaA] mmCIF format, chain N [auth BaB] mmCIF format, chain T [auth DaD] mmCIF format, chain W [auth EaE] mmCIF format, chain Z [auth FaF] mmCIF format, chain Q [auth CaC]	CA [auth GaG] FA [auth HaH] K [auth AaA] N [auth BaB] Q [auth CaC] CA [auth GaG], FA [auth HaH], K [auth AaA], N [auth BaB], Q [auth CaC], T [auth DaD], W [auth EaE], Z [auth FaF]	octa-anionic calixarene C₃₈ H₃₇ As Na O₂₅ S₄ DWJVHZAMZXSDQE-UHFFFAOYSA-M		Interactions Focus chain CA [auth GaG] Focus chain FA [auth HaH] Focus chain K [auth AaA] Focus chain N [auth BaB] Focus chain Q [auth CaC] Focus chain T [auth DaD] Focus chain W [auth EaE] Focus chain Z [auth FaF] Interactions & Density Focus chain CA [auth GaG] Focus chain FA [auth HaH] Focus chain K [auth AaA] Focus chain N [auth BaB] Focus chain Q [auth CaC] Focus chain T [auth DaD] Focus chain W [auth EaE] Focus chain Z [auth FaF]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain J [auth AaA] SDF format, chain M [auth BaB] SDF format, chain P [auth CaC] SDF format, chain S [auth DaD] SDF format, chain V [auth EaE] SDF format, chain Y [auth FaF] SDF format, chain EA [auth HaH] SDF format, chain BA [auth GaG] MOL2 format, chain J [auth AaA] MOL2 format, chain M [auth BaB] MOL2 format, chain P [auth CaC] MOL2 format, chain S [auth DaD] MOL2 format, chain V [auth EaE] MOL2 format, chain Y [auth FaF] MOL2 format, chain EA [auth HaH] MOL2 format, chain BA [auth GaG] mmCIF format, chain J [auth AaA] mmCIF format, chain M [auth BaB] mmCIF format, chain P [auth CaC] mmCIF format, chain S [auth DaD] mmCIF format, chain V [auth EaE] mmCIF format, chain Y [auth FaF] mmCIF format, chain EA [auth HaH] mmCIF format, chain BA [auth GaG]	BA [auth GaG] EA [auth HaH] J [auth AaA] M [auth BaB] P [auth CaC] BA [auth GaG], EA [auth HaH], J [auth AaA], M [auth BaB], P [auth CaC], S [auth DaD], V [auth EaE], Y [auth FaF]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain BA [auth GaG] Focus chain EA [auth HaH] Focus chain J [auth AaA] Focus chain M [auth BaB] Focus chain P [auth CaC] Focus chain S [auth DaD] Focus chain V [auth EaE] Focus chain Y [auth FaF] Interactions & Density Focus chain BA [auth GaG] Focus chain EA [auth HaH] Focus chain J [auth AaA] Focus chain M [auth BaB] Focus chain P [auth CaC] Focus chain S [auth DaD] Focus chain V [auth EaE] Focus chain Y [auth FaF]
ACE Query on ACE Download:Ideal Coordinates CCD File SDF format, chain AA [auth GaG] SDF format, chain DA [auth HaH] SDF format, chain I [auth AaA] SDF format, chain L [auth BaB] SDF format, chain O [auth CaC] SDF format, chain R [auth DaD] SDF format, chain U [auth EaE] SDF format, chain X [auth FaF] MOL2 format, chain AA [auth GaG] MOL2 format, chain DA [auth HaH] MOL2 format, chain I [auth AaA] MOL2 format, chain L [auth BaB] MOL2 format, chain O [auth CaC] MOL2 format, chain R [auth DaD] MOL2 format, chain U [auth EaE] MOL2 format, chain X [auth FaF] mmCIF format, chain AA [auth GaG] mmCIF format, chain DA [auth HaH] mmCIF format, chain I [auth AaA] mmCIF format, chain L [auth BaB] mmCIF format, chain O [auth CaC] mmCIF format, chain R [auth DaD] mmCIF format, chain U [auth EaE] mmCIF format, chain X [auth FaF]	AA [auth GaG] DA [auth HaH] I [auth AaA] L [auth BaB] O [auth CaC] AA [auth GaG], DA [auth HaH], I [auth AaA], L [auth BaB], O [auth CaC], R [auth DaD], U [auth EaE], X [auth FaF]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain AA [auth GaG] Focus chain DA [auth HaH] Focus chain I [auth AaA] Focus chain L [auth BaB] Focus chain O [auth CaC] Focus chain R [auth DaD] Focus chain U [auth EaE] Focus chain X [auth FaF] Interactions & Density Focus chain AA [auth GaG] Focus chain DA [auth HaH] Focus chain I [auth AaA] Focus chain L [auth BaB] Focus chain O [auth CaC] Focus chain R [auth DaD] Focus chain U [auth EaE] Focus chain X [auth FaF]

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

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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