Carminomycin-4-O-methyltransferase (dnrk) variant (298SER insert) in complex with S-adenosyl-L-homocysteine (sah) and aclacinomycin T

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
• 3VL · methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 5 copies · chains A, B
• DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3469 Ų buried · 35 hydrogen bonds · protein-protein

Compared structures

• 4WXH · Carminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert) in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
• Q06528 · AlphaFold monomer V2.0 prediction for carminomycin 4-O-methyltransferase dnrk (Q06528) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q06528
• Elsewhere: RCSB PDB 4WXH · PDBe 4WXH · UniProt Q06528