› 5okd

X-ray diffraction
3.1Å resolution

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.

Released:
DOI: 10.2210/pdb5okd/pdb
PDB entry 5okd coloured by chain, front view.
PDB entry 5okd coloured by chain, side view.
PDB entry 5okd coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
X-ray and cryo-EM structures of inhibitor-bound cytochrome bc1 complexes for structure-based drug discovery.
Amporndanai K, Johnson RM, O'Neill PM, Fishwick CWG, Jamson AH, Rawson S, Muench SP, Hasnain SS, Antonyuk SV
IUCrJ 5 200-210 (2018)
PMID: 29765610

Function and Biology Details

Reaction catalysed: 
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-132256 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 480 amino acids
Theoretical weight: 52.84 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31800 (Residues: 1-480; Coverage: 100%)
Gene name: UQCRC1
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Cytochrome b-c1 complex subunit 2, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 453 amino acids
Theoretical weight: 48.2 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23004 (Residues: 1-453; Coverage: 100%)
Gene name: UQCRC2
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Cytochrome b Chain: C
Molecule details ›
Chain: C
Length: 379 amino acids
Theoretical weight: 42.62 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00157 (Residues: 1-379; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
Structure domains: Cytochrome Bc1 Complex; Chain C
Cytochrome c1, heme protein, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 325 amino acids
Theoretical weight: 35.34 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00125 (Residues: 1-325; Coverage: 100%)
Gene name: CYC1
Sequence domains: Cytochrome C1 family
Structure domains:
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 196 amino acids
Theoretical weight: 21.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 79-274; Coverage: 72%)
Gene name: UQCRFS1
Sequence domains:
Structure domains:
Cytochrome b-c1 complex subunit 7 Chain: F
Molecule details ›
Chain: F
Length: 111 amino acids
Theoretical weight: 13.5 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00129 (Residues: 1-111; Coverage: 100%)
Gene name: UQCRB
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Structure domains: Cytochrome b-c1 complex subunit 7
Cytochrome b-c1 complex subunit 8 Chain: G
Molecule details ›
Chain: G
Length: 82 amino acids
Theoretical weight: 9.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13271 (Residues: 1-82; Coverage: 100%)
Gene name: UQCRQ
Sequence domains: UcrQ family
Structure domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 91 amino acids
Theoretical weight: 10.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00126 (Residues: 1-91; Coverage: 100%)
Gene name: UQCRH
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Structure domains: Ubiquinol-cytochrome C reductase hinge domain
Cytochrome b-c1 complex subunit 9 Chain: I
Molecule details ›
Chain: I
Length: 47 amino acids
Theoretical weight: 4.9 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 32-78; Coverage: 17%)
Gene name: UQCRFS1
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Structure domains: Cytochrome Bc1 Complex; Chain I
Cytochrome b-c1 complex subunit 9 Chain: J
Molecule details ›
Chain: J
Length: 64 amino acids
Theoretical weight: 7.47 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00130 (Residues: 1-64; Coverage: 100%)
Gene name: UQCR10
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Structure domains: Cytochrome b-c1 complex subunit 9

Ligands and Environments

11 bound ligands:
Ligand PG4 3 x PG4
Ligand 6PE 1 x 6PE
Ligand CDL 4 x CDL
Ligand HEM 2 x HEM
Ligand 9XE 1 x 9XE
Ligand LMT 1 x LMT
Ligand PEE 2 x PEE
Ligand HEC 1 x HEC
Ligand PO4 6 x PO4
Ligand FES 1 x FES
Ligand PX4 1 x PX4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P6522
Unit cell:
a: 209.871Å b: 209.871Å c: 342.097Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.205 0.24

Quick links

Citations

3 review citations

Tuberculosis: Past, present and future of the treatment and drug discovery research.
Bendre et al. (2021)
2 more

5 mentions without citation

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy.
Kao et al. (2022)
4 more