› 4d6u

X-ray diffraction
4.09Å resolution

Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121

Released:
DOI: 10.2210/pdb4d6u/pdb
PDB entry 4d6u coloured by chain, front view.
PDB entry 4d6u coloured by chain, side view.
PDB entry 4d6u coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Antimalarial 4(1H)-pyridones bind to the Qi site of cytochrome bc1.
Capper MJ, O'Neill PM, Fisher N, Strange RW, Moss D, Ward SA, Berry NG, Lawrenson AS, Hasnain SS, Biagini GA, Antonyuk SV
Proc Natl Acad Sci U S A 112 755-60 (2015)
PMID: 25564664

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:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 480 amino acids
Theoretical weight: 52.8 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31800 (Residues: 1-480; Coverage: 100%)
Gene name: UQCRC1
Sequence domains:
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:
Cytochrome b Chains: C, P
Molecule details ›
Chains: C, P
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:
Cytochrome c1, heme protein, mitochondrial Chains: D, Q
Molecule details ›
Chains: D, Q
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
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, I, R
Molecule details ›
Chains: E, I, R
Length: 274 amino acids
Theoretical weight: 29.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 1-274; Coverage: 100%)
Gene name: UQCRFS1
Sequence domains:
Cytochrome b-c1 complex subunit 7 Chains: F, S
Molecule details ›
Chains: F, S
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
Cytochrome b-c1 complex subunit 8 Chains: G, T
Molecule details ›
Chains: G, T
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
Cytochrome b-c1 complex subunit 6, mitochondrial Chains: H, U
Molecule details ›
Chains: H, U
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
Cytochrome b-c1 complex subunit 9 Chains: J, W
Molecule details ›
Chains: J, W
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
Cytochrome b-c1 complex subunit 1, mitochondrial Chain: N
Molecule details ›
Chain: N
Length: 480 amino acids
Theoretical weight: 52.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31800 (Residues: 1-480; Coverage: 100%)
Gene name: UQCRC1
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chain: O
Molecule details ›
Chain: O
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:
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 274 amino acids
Theoretical weight: 29.57 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 1-274; Coverage: 100%)
Gene name: UQCRFS1
Sequence domains:

Ligands and Environments

8 bound ligands:
Ligand HEM 4 x HEM
Ligand G8U 2 x G8U
Ligand PO4 9 x PO4
Ligand PEE 4 x PEE
Ligand HEC 2 x HEC
Ligand CDL 4 x CDL
Ligand FES 1 x FES
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P65
Unit cell:
a: 129.49Å b: 129.49Å c: 719.936Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.223 0.271

Quick links

Citations

7 review citations

Malaria medicines: a glass half full?
Wells et al. (2015)
6 more

9 mentions without citation

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