Research workbench
Nitroalkane oxidase: active site mutant S276A crystallized with 1- nitrohexane
Analyse Nitroalkane oxidase: active site mutant S276A crystallized with 1- nitrohexane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D9F
- Type
- protein
- Length
- 1,722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroalkane oxidase
- EC
- 1.7.3.1
- UniProt
- Q8X1D8
- Ligands
- FAD, N6C
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitroalkane oxidase (EC 1.7.3.1) | protein | 431 | 54% helix, 12% strand | Q8X1D8 |
| C, D | Nitroalkane oxidase (EC 1.7.3.1) | protein | 430 | 53% helix, 12% strand | Q8X1D8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- N6C · 1-nitrohexane · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.88 | 0.89 | 141 | FAD, N6C, GOL |
| 2 | 700 | 0.85 | 0.89 | 87 | FAD, N6C, GOL |
| 3 | 715 | 0.85 | 0.89 | 85 | FAD, N6C, GOL |
| 4 | 881 | 0.83 | 0.85 | 98 | FAD, N6C, GOL |
| 5 | 481 | 0.64 | 0.77 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2723 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2717 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2137 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2130 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3D9F · Nitroalkane oxidase: active site mutant S276A crystallized with 1-nitrohexane · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X1D8 · AlphaFold monomer V2.0 prediction for nitroalkane oxidase (Q8X1D8) · a predicted model of the same protein · chain A 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 Q8X1D8
- Elsewhere: RCSB PDB 3D9F · PDBe 3D9F · UniProt Q8X1D8
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