MolNFT v1 · #32797 · protein
Crystal structure of nitroalkane oxidase in complex with spermine, a competitive inhibitor
2C12: “Crystal structure of nitroalkane oxidase in complex with spermine, a competitive inhibitor”. X-ray diffraction, 2 ligands (FAD, SPM), 20 pockets (best druggability 0.86). MolNFT v1 #32797 on GenesisL1: 3D structure, binding sites…
- PDB
- 2C12
- Type
- protein
- Length
- 2,580 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroalkane oxidase
- UniProt
- Q8X1D8
- Ligands
- FAD, SPM
- 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, E, F | Nitroalkane oxidase | protein | 430 | 53% helix, 12% strand | Q8X1D8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SPM · Spermine · ligand · 4 copies · chains B, C, D, F
- GOL · Glycerol · additive · 15 copies · chains A, B, D, C, E, F
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.86 | 0.91 | 86 | FAD, SPM |
| 2 | 721 | 0.86 | 0.90 | 89 | FAD, SPM |
| 3 | 780 | 0.86 | 0.88 | 92 | FAD, SPM |
| 4 | 748 | 0.85 | 0.88 | 89 | FAD |
| 5 | 625 | 0.85 | 0.90 | 72 | FAD |
Interfaces
7 interfaces between chains.
- A–C · 2716 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 2712 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2146 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2127 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2110 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2C12 · Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor · the same entry in another collection · chain E against E, 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 2C12 · PDBe 2C12 · UniProt Q8X1D8
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