Research workbench
Crystal structure of SULFIDE:QUINONE oxidoreductase CYS128SER variant from acidithiobacillus ferrooxidans in complex with decylubiquinone
Analyse Crystal structure of SULFIDE:QUINONE oxidoreductase CYS128SER variant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZW
- Type
- protein
- Length
- 421 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfide-quinone reductase, putative
- UniProt
- B7JBP8
- Ligands
- FAD, DCQ, H2S, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfide-quinone reductase, putative | protein | 421 | 30% helix, 27% strand | B7JBP8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · chains A
- H2S · Hydrosulfuric acid · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.83 | 0.83 | 78 | FAD, DCQ, H2S |
| 2 | 160 | 0.64 | 0.85 | 27 | empty |
| 3 | 169 | 0.53 | 0.79 | 30 | empty |
| 4 | 63 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 3SZW · Crystal structure of sulfide:qui oxidoreductase Cys128Ser variant from Acidithiobacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- B7JBP8 · AlphaFold monomer V2.0 prediction for sulfide-quinone reductase (B7JBP8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 B7JBP8
- Elsewhere: RCSB PDB 3SZW · PDBe 3SZW · UniProt B7JBP8
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