Crystal structure of quercetin 2,3-dioxygenase anaerobically complexed with the substrate kaempferol

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 37% strand (DSSP).

Ligands and binding sites

• KMP · 3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, C, B, D
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, D, A
• BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, D, A
• CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, B, 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, 11 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–D · 2163 Ų buried · 35 hydrogen bonds · protein-protein
• A–C · 2156 Ų buried · 37 hydrogen bonds · protein-protein
• B–C · 553 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 glycan (N-glycosylation).

Compared structures

• 1H1M · Crystal structure of quercetin 2,3-dioxygenase anaerobically complexed with the substrate… · the same entry in another collection · chain A against A, TM-score 1.00
• Q7SIC2 · AlphaFold monomer V2.0 prediction for quercetin 2,3-dioxygenase (Q7SIC2) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q7SIC2
• Elsewhere: RCSB PDB 1H1M · PDBe 1H1M · UniProt Q7SIC2