3VRA

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor Atpenin A5

• PDB DOI: https://doi.org/10.2210/pdb3VRA/pdb

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


• Deposited: 2012-04-07 Released: 2013-04-10 
• Deposition Author(s): Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free: 0.281 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Crystal structure of mitochondrial quinol-fumarate reductase from parasitic nematode Ascaris suum

Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

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: 289.13 kDa 
• Atom Count: 18,262 
• Modelled Residue Count: 2,288 
• Deposited Residue Count: 2,542 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein subunit of complex II	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
Iron-sulfur subunit of succinate dehydrogenase	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	J [auth A], R [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
EPH	P [auth D], X [auth H]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C39 H68 N O8 P MABRTXOVHMDVAT-AAEGOEIASA-N
HEM	N [auth C], V [auth G]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
AT5	O [auth C], W [auth G]	3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE C15 H21 Cl2 N O5 OVULNOOPECCZRG-CIUDSAMLSA-N
SF4	L [auth B], T [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	M [auth B], U [auth F]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES	K [auth B], S [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI	I [auth A], Q [auth E]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free: 0.281 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.823	α = 90
b = 132.25	β = 90
c = 220.577	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description