Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase (hod) catalytically inactive H251A variant complexed with its natural substrate 1-H-3- hydroxy-4-oxoquinaldine

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Ligands and binding sites

• HQD · 3-hydroxy-2-methylquinolin-4(1H)-one · ligand · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · 4 copies · chains A, B, C, D
• TAR · D(-)-tartaric acid · additive · 7 copies · chains A, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 636 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 567 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 538 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 4CFS · Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase… · the same entry in another collection · chain A against A, TM-score 1.00
• O31266 · AlphaFold monomer V2.0 prediction for 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase… · a predicted model of the same protein · chain D 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 O31266
• Elsewhere: RCSB PDB 4CFS · PDBe 4CFS · UniProt O31266