Research workbench
3-D X-ray structure of the SULFIDE:QUINONE oxidoreductase from the hyperthermophilic bacterium aquifex aeolicus
Analyse 3-D X-ray structure of the SULFIDE:QUINONE oxidoreductase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYV
- Type
- protein
- Length
- 2,574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfide-quinone reductase
- EC
- 1.8.5.-
- UniProt
- O67931
- Ligands
- PS9, FAD, SO4, H2S
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Sulfide-quinone reductase (EC 1.8.5.-) | protein | 429 | 31% helix, 26% strand | O67931 |
Ligands and binding sites
- PS9 · octathiocane · ligand · 7 copies · chains A, B, C, D, E, F
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 24 copies · chains A, E, B, D, F, C
- H2S · Hydrosulfuric acid · ion · 6 copies · chains A, B, C, D, E, F
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.86 | 0.93 | 83 | FAD, H2S, PS9 |
| 2 | 441 | 0.86 | 0.92 | 74 | FAD, H2S, PS9 |
| 3 | 446 | 0.86 | 0.93 | 76 | FAD, H2S, PS9 |
| 4 | 394 | 0.85 | 0.93 | 70 | FAD, H2S, PS9 |
| 5 | 404 | 0.85 | 0.93 | 74 | FAD, H2S, PS9 |
Interfaces
9 interfaces between chains.
- A–B · 761 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 746 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 710 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 660 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 modified (disulfide, oxidation).
Compared structures
- 3HYV · 3-D X-Ray structure of the sulfide:qui oxidoreductase from the hyperthermophilic… · the same entry in another collection · chain C against C, TM-score 1.00
- O67931 · AlphaFold monomer V2.0 prediction for sulfide-quinone reductase (O67931) · 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 O67931
- Elsewhere: RCSB PDB 3HYV · PDBe 3HYV · UniProt O67931
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