Crystal structure of nitroalkane oxidase in complex with spermine, a competitive inhibitor

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).

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.

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