Crystal structure of KIJD10, a 3-ketoreductase from actinomadura kijaniata in complex with tdp-benzene and NADP; open conformation

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).

Ligands and binding sites

• TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · ligand · chains A
• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 2 copies · chains A
• PO4 · Phosphate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Compared structures

• 3RC2 · Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex… · the same entry in another collection · chain A against A, TM-score 1.00
• B3TMR8 · AlphaFold monomer V2.0 prediction for dtdp-3,4-didehydro-2,6-dideoxy- alpha-D-glucose… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 B3TMR8
• Elsewhere: RCSB PDB 3RC2 · PDBe 3RC2 · UniProt B3TMR8