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 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase flavoprotein
A, E
645N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B, F
282Ascaris suumMutation(s): 0 
EC: 1.3.5.1
Find proteins for O44074 (Ascaris suum)
Go to UniProtKB:  O44074
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-large subunit
C, G
188Ascaris suumMutation(s): 0 
Find proteins for F1LC27 (Ascaris suum)
Go to UniProtKB:  F1LC27
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D, H
156Ascaris suumMutation(s): 0 
Find proteins for P92507 (Ascaris suum)
Go to UniProtKB:  P92507
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FD8
Query on FD8

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Download CCD File 
C, F
N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide
C20 H9 F8 N O2
ZTJJBXFGRJEBCQ-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MLI
Query on MLI

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Download CCD File 
A, E
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, E
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
B, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C, G
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 123.614α = 90.00
b = 125.483β = 90.00
c = 219.670γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release