Structure of TYLM1 from streptomyces fradiae H123N mutant in complex with sah and dtdp-QUIP3N

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 38% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
• T3Q · [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 2 copies · chains A, D
• EDO · 1,2-ethanediol · additive · 2 copies · chains D

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

Pockets

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

Interfaces

1 interface between chains.

• A–D · 784 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 3PX2 · Structure of TylM1 from Streptomyces fradiae H123N mutant in complex with SAH and… · the same entry in another collection · chain A against A, TM-score 1.00
• P95748 · AlphaFold monomer V2.0 prediction for dtdp-3-amino-3,6-dideoxy-alpha- D-glucopyranose… · a predicted model of the same protein · chain D 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 P95748
• Elsewhere: RCSB PDB 3PX2 · PDBe 3PX2 · UniProt P95748