Research workbench
Crystal structure of the selenomethionine-substituted human SULFIDE:QUINONE oxidoreductase
Analyse Crystal structure of the selenomethionine-substituted human SULFIDE:QUINONE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MO6
- Type
- protein
- Length
- 1,654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SULFIDE:QUINONE oxidoreductase, mitochondrial
- EC
- 1.8.5.-
- UniProt
- Q9Y6N5
- Ligands
- FAD, CL
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SULFIDE:QUINONE oxidoreductase, mitochondrial (EC 1.8.5.-) | protein | 413 | 33% helix, 27% strand | Q9Y6N5 |
| B, C | SULFIDE:QUINONE oxidoreductase, mitochondrial (EC 1.8.5.-) | protein | 414 | 34% helix, 27% strand | Q9Y6N5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.82 | 0.85 | 77 | FAD |
| 2 | 764 | 0.82 | 0.85 | 71 | FAD |
| 3 | 727 | 0.81 | 0.85 | 68 | FAD |
| 4 | 747 | 0.81 | 0.84 | 69 | FAD |
| 5 | 374 | 0.65 | 0.79 | 33 | empty |
Interfaces
3 interfaces between chains.
- C–D · 500 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered, oxidation).
Compared structures
- 6MO6 · Crystal structure of the selenomethionine-substituted human sulfide:qui oxidoreductase · 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 A against A, TM-score 0.99
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 6MO6 · PDBe 6MO6 · UniProt Q9Y6N5
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