› 6myt

X-ray diffraction
2.27Å resolution

Avian mitochondrial complex II with Atpenin A5 bound, sidechain in pocket

Released:
DOI: 10.2210/pdb6myt/pdb
PDB entry 6myt coloured by chain, front view.
PDB entry 6myt coloured by chain, side view.
PDB entry 6myt coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.
Huang LS, Lümmen P, Berry EA
Biochim Biophys Acta Proteins Proteom 1869 140679 (2021)
PMID: 34089891

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-112133 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 621 amino acids
Theoretical weight: 68.26 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q9YHT1 (Residues: 45-665; Coverage: 93%)
Gene name: SDHA
Sequence domains:
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 252 amino acids
Theoretical weight: 28.69 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q9YHT2 (Residues: 39-290; Coverage: 87%)
Gene name: SDHB
Sequence domains:
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 140 amino acids
Theoretical weight: 15.39 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VWW3 (Residues: 1-140; Coverage: 100%)
Sequence domains: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 103 amino acids
Theoretical weight: 10.97 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q5ZIS0 (Residues: 55-157; Coverage: 66%)
Gene names: RCJMB04_23p7, SDHD
Sequence domains: CybS, succinate dehydrogenase cytochrome B small subunit

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM

Cofactor: Ligand AT5 1 x AT5

Cofactor: Ligand FAD 1 x FAD
9 bound ligands:
Ligand OAA 1 x OAA
Ligand K 1 x K
Ligand UNL 59 x UNL
Ligand PEG 1 x PEG
Ligand FES 1 x FES
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand UMQ 1 x UMQ
Ligand 3PE 1 x 3PE
1 modified residue:
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 69.992Å b: 83.817Å c: 290.344Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.226 0.26

Quick links

Citations

3 review citations

Succinate Dehydrogenase, Succinate, and Superoxides: A Genetic, Epigenetic, Metabolic, Environmental Explosive Crossroad.
Bénit et al. (2022)
2 more

1 mention without citation

Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.
Huang et al. (2021)