› 4yxd

X-ray diffraction
3Å resolution

CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH flutolanil

Released:
DOI: 10.2210/pdb4yxd/pdb
PDB entry 4yxd coloured by chain, front view.
PDB entry 4yxd coloured by chain, side view.
PDB entry 4yxd coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria.
Inaoka DK, Shiba T, Sato D, Balogun EO, Sasaki T, Nagahama M, Oda M, Matsuoka S, Ohmori J, Honma T, Inoue M, Kita K, Harada S
Int J Mol Sci 16 15287-308 (2015)
PMID: 26198225

Function and Biology Details

Reaction catalysed: 
Succinate + a quinone = fumarate + a quinol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-107594 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 664 amino acids
Theoretical weight: 72.93 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q0QF01 (Residues: 1-664; Coverage: 100%)
Gene name: SDHA
Sequence domains:
Structure domains:
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 280 amino acids
Theoretical weight: 31.63 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q007T0 (Residues: 1-280; Coverage: 100%)
Gene name: SDHB
Sequence domains:
Structure domains:
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 169 amino acids
Theoretical weight: 18.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D0VWV4 (Residues: 1-169; Coverage: 100%)
Gene name: SDHC
Sequence domains: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Structure domains:
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 159 amino acids
Theoretical weight: 17.03 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A5GZW8 (Residues: 1-159; Coverage: 100%)
Gene name: SDHD
Sequence domains: CybS, succinate dehydrogenase cytochrome B small subunit
Structure domains: Fumarate reductase/succinate dehydrogenase, transmembrane subunit

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD

Cofactor: Ligand HEM 1 x HEM
4 bound ligands:
Ligand FES 1 x FES
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand FTN 1 x FTN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 70.366Å b: 83.746Å c: 292.625Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.258

Quick links

Citations

2 review citations

Why All the Fuss about Oxidative Phosphorylation (OXPHOS)?
Xu et al. (2020)
1 more

5 mentions without citation

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.
Schweppe et al. (2017)
4 more