MolNFT v1 · #32790 · protein
Crystal structure of a covalent complex of nitroalkane oxidase trapped during substrate turnover
2C0U: “Crystal structure of a covalent complex of nitroalkane oxidase trapped during substrate turnover”. X-ray diffraction, 2 ligands (FAD, NBT), 19 pockets (best druggability 0.86). MolNFT v1 #32790 on GenesisL1: 3D structure, binding…
- PDB
- 2C0U
- Type
- protein
- Length
- 1,720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroalkane oxidase
- UniProt
- Q8X1D8
- Ligands
- FAD, NBT
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nitroalkane oxidase | protein | 430 | 55% helix, 11% strand | Q8X1D8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NBT · (2S)-2-nitrobutane · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.86 | 0.91 | 82 | FAD, NBT |
| 2 | 613 | 0.86 | 0.91 | 90 | FAD, NBT |
| 3 | 616 | 0.86 | 0.90 | 81 | FAD, NBT |
| 4 | 599 | 0.85 | 0.90 | 72 | FAD, NBT |
| 5 | 1163 | 0.82 | 0.83 | 72 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2725 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2687 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2145 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2145 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 204 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 2C0U · Crystal Structure of a Covalent Complex of Nitroalkane Oxidase Trapped During Substrate… · 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 2C0U · PDBe 2C0U · UniProt Q8X1D8
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