X-ray structure of the KIJD1 C3-methyltransferase from actinomadura kijaniata in complex with sah and dtdp-sugar product

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
• JHZ · (2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A
• CL · Chloride ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 955 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 5T67 · x-ray structure of the KijD1 C3-methyltransferase from Actinomadura kijaniata in complex… · the same entry in another collection · 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 B3TMQ9
• Elsewhere: RCSB PDB 5T67 · PDBe 5T67 · UniProt B3TMQ9