MolNFT v1 · #56284 · protein
Mechanistic and structural analyses of the roles of ARG409 and ASP402 in the reaction of the flavoprotein nitroalkane oxidase
2ZAF: “Mechanistic and structural analyses of the roles of ARG409 and ASP402 in the reaction of the flavoprotein…”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.86). MolNFT v1 #56284 on GenesisL1: 3D structure…
- PDB
- 2ZAF
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.86 | 0.89 | 86 | FAD |
| 2 | 637 | 0.86 | 0.90 | 83 | FAD |
| 3 | 661 | 0.85 | 0.89 | 83 | FAD |
| 4 | 719 | 0.85 | 0.89 | 79 | FAD |
| 5 | 1188 | 0.83 | 0.84 | 73 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2730 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2724 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2177 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2155 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2ZAF · 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 2ZAF · PDBe 2ZAF · UniProt Q8X1D8
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