Research workbench
Mechanistic and structural analyses of the roles of ARG409 and ASP402 in the reaction of the flavoprotein nitroalkane oxidase
Analyse Mechanistic and structural analyses of the roles of ARG409 and ASP402 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2REH
- Type
- protein
- Length
- 1,720 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
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.86 | 0.93 | 72 | FAD |
| 2 | 502 | 0.85 | 0.92 | 71 | FAD |
| 3 | 727 | 0.84 | 0.88 | 90 | FAD |
| 4 | 609 | 0.84 | 0.89 | 79 | FAD |
| 5 | 154 | 0.67 | 0.89 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2748 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2735 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2132 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2117 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2REH · Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of… · 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 2REH · PDBe 2REH · UniProt Q8X1D8
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