3VRA

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


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
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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

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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavoprotein subunit of complex II
A, E
645Ascaris suumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ33862
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur subunit of succinate dehydrogenase
B, F
282Ascaris suumMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO44074
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-large subunit
C, G
188Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92506 (Ascaris suum)
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Go to UniProtKB:  P92506
Entity Groups  
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UniProt GroupP92506
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D, H
156Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92507 (Ascaris suum)
Explore P92507 
Go to UniProtKB:  P92507
Entity Groups  
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UniProt GroupP92507
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
J [auth A],
R [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EPH
Query on EPH

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P [auth D],
X [auth H]
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
N [auth C],
V [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
AT5
Query on AT5

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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
Query on SF4

Download Ideal Coordinates CCD File 
L [auth B],
T [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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M [auth B],
U [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
K [auth B],
S [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
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 = 122.823α = 90
b = 132.25β = 90
c = 220.577γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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