5C3J

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with Ubiquinone-1

PDB DOI: https://doi.org/10.2210/pdb5C3J/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Ascaris suum
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2015-06-17 Released: 2016-06-22
Deposition Author(s): Harada, S., Shiba, T., Sato, D., Yamamoto, A., Nagahama, M., Yone, A., Inaoka, D.K., Sakamoto, K., Inoue, M., Honma, T., Kita, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.260
R-Value Work: 0.202
R-Value Observed: 0.205

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

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

Harada, S., Shiba, T., Sato, D., Yamamoto, A., Nagahama, M., Yone, A., Inaoka, D.K., Sakamoto, K., Inoue, M., Honma, T., Kita, K.

To be published.

Macromolecule Content

Total Structure Weight: 289.07 kDa
Atom Count: 18,342
Modelled Residue Count: 2,296
Deposited Residue Count: 2,542
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A, E	645	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q33862 (Ascaris suum) Explore Q33862 Go to UniProtKB: Q33862
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q33862
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B, F	282	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for O44074 (Ascaris suum) Explore O44074 Go to UniProtKB: O44074
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O44074
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-large subunit	C, G	188	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92506 (Ascaris suum) Explore P92506 Go to UniProtKB: P92506
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P92506
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D, H	156	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92507 (Ascaris suum) Explore P92507 Go to UniProtKB: P92507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P92507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth E] MOL2 format, chain J [auth A] MOL2 format, chain R [auth E] mmCIF format, chain J [auth A] mmCIF format, chain R [auth E]	J [auth A], R [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain J [auth A] Focus chain R [auth E] Interactions & Density Focus chain J [auth A] Focus chain R [auth E]
EPH Query on EPH Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain X [auth H] MOL2 format, chain P [auth D] MOL2 format, chain X [auth H] mmCIF format, chain P [auth D] mmCIF format, chain X [auth H]	P [auth D], X [auth H]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Interactions Focus chain P [auth D] Focus chain X [auth H] Interactions & Density Focus chain P [auth D] Focus chain X [auth H]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain V [auth G] MOL2 format, chain N [auth C] MOL2 format, chain V [auth G] mmCIF format, chain N [auth C] mmCIF format, chain V [auth G]	N [auth C], V [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth C] Focus chain V [auth G] Interactions & Density Focus chain N [auth C] Focus chain V [auth G]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth F] MOL2 format, chain L [auth B] MOL2 format, chain T [auth F] mmCIF format, chain L [auth B] mmCIF format, chain T [auth F]	L [auth B], T [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth F] Interactions & Density Focus chain L [auth B] Focus chain T [auth F]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain U [auth F] MOL2 format, chain M [auth B] MOL2 format, chain U [auth F] mmCIF format, chain M [auth B] mmCIF format, chain U [auth F]	M [auth B], U [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain U [auth F] Interactions & Density Focus chain M [auth B] Focus chain U [auth F]
UQ1 Query on UQ1 Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain W [auth G] MOL2 format, chain O [auth C] MOL2 format, chain W [auth G] mmCIF format, chain O [auth C] mmCIF format, chain W [auth G]	O [auth C], W [auth G]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain W [auth G] Interactions & Density Focus chain O [auth C] Focus chain W [auth G]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain S [auth F] MOL2 format, chain K [auth B] MOL2 format, chain S [auth F] mmCIF format, chain K [auth B] mmCIF format, chain S [auth F]	K [auth B], S [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain S [auth F] Interactions & Density Focus chain K [auth B] Focus chain S [auth F]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth E]	I [auth A], Q [auth E]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain Q [auth E] Interactions & Density Focus chain I [auth A] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.260
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.75	α = 90
b = 126.827	β = 90
c = 220.449	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5C3J

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with Ubiquinone-1

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 4

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)