4YTN

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide

• PDB DOI: https://doi.org/10.2210/pdb4YTN/pdb

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


• Deposited: 2015-03-18 Released: 2015-08-05 
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

New Insights into the Design of Inhibitors Targeted for Parasitic Anaerobic Energy Metabolism

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 288.05 kDa 
• Atom Count: 18,320 
• Modelled Residue Count: 2,296 
• Deposited Residue Count: 2,542 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase flavoprotein	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 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 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 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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	J [auth A], Q [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	N [auth C], V [auth G]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FD8	O [auth C], U [auth F]	N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide C20 H9 F8 N O2 ZTJJBXFGRJEBCQ-UHFFFAOYSA-N
SF4	L [auth B], S [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	M [auth B], T [auth F]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES	K [auth B], R [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI	I [auth A], P [auth E]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.614	α = 90
b = 125.483	β = 90
c = 219.67	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
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.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary