Structure and mechanisim of core 2 BETA1,6-N- acetylglucosaminyltransferase: a metal-ion independent gt-a glycosyltransferase

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).

Ligands and binding sites

• UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
• HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
• NA · Sodium ion · metal · 2 copies · chains A, C

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 998 Ų buried · 8 hydrogen bonds · protein-protein
• C–D · 993 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 316 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 3OTK · Structure and mechanisim of core 2 beta1,6-n-acetylglucosaminyltransferase: a Metal-ion… · the same entry in another collection · chain D against D, TM-score 1.00
• Q09324 · AlphaFold monomer V2.0 prediction for beta-1,3-galactosyl-O-glycosyl- glycoprotein… · a predicted model of the same protein · chain C 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 Q09324
• Elsewhere: RCSB PDB 3OTK · PDBe 3OTK · UniProt Q09324