Research workbench
Crystal structure of human sulfide quinone oxidoreductase in complex with coenzyme Q (cyanide soaked)
Analyse Crystal structure of human sulfide quinone oxidoreductase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WH6
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SULFIDE:QUINONE oxidoreductase, mitochondrial
- EC
- 1.8.5.-
- UniProt
- Q9Y6N5
- Ligands
- UQ1, FAD, CYN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SULFIDE:QUINONE oxidoreductase, mitochondrial (EC 1.8.5.-) | protein | 407 | 34% helix, 28% strand | Q9Y6N5 |
| B | SULFIDE:QUINONE oxidoreductase, mitochondrial (EC 1.8.5.-) | protein | 405 | 34% helix, 27% strand | Q9Y6N5 |
Ligands and binding sites
- UQ1 · Ubiquinone-1 · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.82 | 0.85 | 70 | FAD, UQ1 |
| 2 | 737 | 0.81 | 0.84 | 73 | FAD, UQ1 |
| 3 | 1043 | 0.79 | 0.80 | 123 | empty |
| 4 | 81 | 0.37 | 0.77 | 19 | empty |
| 5 | 74 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1098 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6WH6 · Crystal structure of human sulfide qui oxidoreductase in complex with coenzyme Q (cyanide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6N5 · AlphaFold monomer V2.0 prediction for SULFIDE:QUINONE oxidoreductase, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y6N5
- Elsewhere: RCSB PDB 6WH6 · PDBe 6WH6 · UniProt Q9Y6N5
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