3SFD

crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and pentachlorophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Thiabendazole inhibits ubiquinone reduction activity of mitochondrial respiratory complex II via a water molecule mediated binding feature.

Zhou, Q.Zhai, Y.Lou, J.Liu, M.Pang, X.Sun, F.

(2011) Protein Cell 2: 531-542

  • DOI: 10.1007/s13238-011-1079-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mitochondrial respiratory complex II or succinate: ubiquinone oxidoreductase (SQR) is a key membrane complex in both the tricarboxylic acid cycle and aerobic respiration. Five disinfectant compounds were investigated with their potent inhibition ...

    The mitochondrial respiratory complex II or succinate: ubiquinone oxidoreductase (SQR) is a key membrane complex in both the tricarboxylic acid cycle and aerobic respiration. Five disinfectant compounds were investigated with their potent inhibition effects on the ubiquinone reduction activity of the porcine mitochondrial SQR by enzymatic assay and crystallography. Crystal structure of the SQR bound with thiabendazole (TBZ) reveals a different inhibitor-binding feature at the ubiquinone binding site where a water molecule plays an important role. The obvious inhibitory effect of TBZ based on the biochemical data (IC(50) ~100 μmol/L) and the significant structure-based binding affinity calculation (~94 μmol/L) draw the suspicion of using TBZ as a good disinfectant compound for nematode infections treatment and fruit storage.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
A
622Sus scrofaMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Find proteins for Q0QF01 (Sus scrofa)
Go to Gene View: SDHA
Go to UniProtKB:  Q0QF01
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B
252Sus scrofaMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Find proteins for Q007T0 (Sus scrofa)
Go to Gene View: SDHB
Go to UniProtKB:  Q007T0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
C
140Sus scrofaMutation(s): 0 
Gene Names: SDHC
Find proteins for D0VWV4 (Sus scrofa)
Go to Gene View: SDHC
Go to UniProtKB:  D0VWV4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D
103Sus scrofaMutation(s): 0 
Gene Names: SDHD
Find proteins for A5GZW8 (Sus scrofa)
Go to Gene View: SDHD
Go to UniProtKB:  A5GZW8
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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

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

Download SDF File 
Download CCD File 
A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PCI
Query on PCI

Download SDF File 
Download CCD File 
D
PENTACHLOROPHENOL
C6 H Cl5 O
IZUPBVBPLAPZRR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.310α = 90.00
b = 83.360β = 90.00
c = 293.100γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release