4YTN

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoproteinA, E645Ascaris suumMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrialB, F282Ascaris suumMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for O44074 (Ascaris suum)
Explore O44074 
Go to UniProtKB:  O44074
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-large subunitC, G188Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1LC27 (Ascaris suum)
Explore F1LC27 
Go to UniProtKB:  F1LC27
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrialD, H156Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92507 (Ascaris suum)
Explore P92507 
Go to UniProtKB:  P92507
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
J [auth A], Q [auth E]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
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
 Ligand Interaction
FD8
Query on FD8

Download Ideal Coordinates CCD File 
O [auth C], U [auth F]N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide
C20 H9 F8 N O2
ZTJJBXFGRJEBCQ-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
L [auth B], S [auth F]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
M [auth B], T [auth F]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

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

Download Ideal Coordinates CCD File 
I [auth A], P [auth E]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
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 = 123.614α = 90
b = 125.483β = 90
c = 219.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations