Research workbench
Nitroalkane oxidase: active site mutant D402N crystallized with 1- nitrooctane
Analyse Nitroalkane oxidase: active site mutant D402N crystallized with 1- nitrooctane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D9E
- Type
- protein
- Length
- 1,723 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, N8C
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Nitroalkane oxidase (EC 1.7.3.1) | protein | 431 | 54% helix, 12% strand | Q8X1D8 |
| C | Nitroalkane oxidase (EC 1.7.3.1) | protein | 430 | 54% helix, 12% strand | Q8X1D8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- N8C · 1-nitrooctane · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.86 | 0.91 | 81 | FAD, N8C, GOL |
| 2 | 582 | 0.86 | 0.91 | 74 | FAD, N8C, GOL |
| 3 | 875 | 0.84 | 0.86 | 102 | FAD, N8C, GOL |
| 4 | 902 | 0.83 | 0.85 | 100 | FAD, N8C, GOL |
| 5 | 1155 | 0.82 | 0.83 | 73 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2723 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2704 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2130 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2129 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3D9E · Nitroalkane oxidase: active site mutant D402N crystallized with 1-nitrooctane · 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 3D9E · PDBe 3D9E · UniProt Q8X1D8
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