MolNFT v1 · #65831 · protein
The first X-ray structure of a SULFIDE:QUINONE oxidoreductase: insights into sulfide oxidation mechanism
3H8I · NADH oxidase: “The first X-ray structure of a SULFIDE:QUINONE oxidoreductase: insights into sulfide oxidation mechanism”. X-ray diffraction, 3 ligands (FAD, S3H, PO4), 6 pockets (best druggability 0.79). MolNFT v1 #65831 on…
- PDB
- 3H8I
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH oxidase
- EC
- 1.6.99.3
- UniProt
- Q7ZAG8
- Ligands
- FAD, S3H, PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADH oxidase (EC 1.6.99.3) | protein | 356 | 29% helix, 27% strand | Q7ZAG8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- S3H · trisulfane · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 9 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.79 | 0.80 | 112 | FAD, S3H, PO4 |
| 2 | 949 | 0.76 | 0.79 | 80 | PO4, FAD |
| 3 | 138 | 0.69 | 0.90 | 31 | S3H |
| 4 | 231 | 0.50 | 0.75 | 29 | PO4 |
| 5 | 196 | 0.48 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1536 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 cofactor (covalent ligand, flavinylation).
Compared structures
- 3H8I · The first X-ray structure of a sulfide:qui oxidoreductase: Insights into sulfide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7ZAG8 · AlphaFold monomer V2.0 prediction for sulfide-quinone reductase (Q7ZAG8) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q7ZAG8
- Elsewhere: RCSB PDB 3H8I · PDBe 3H8I · UniProt Q7ZAG8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.