Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with glcnac- BETA1,2-man-peptide

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 37% strand (DSSP).

Ligands and binding sites

• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, C, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
• NA · Sodium ion · metal · 5 copies · chains A, B

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–B · 390 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 210 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 199 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 glycan (O-glycosylation).

Compared structures

• 5GGP · Crystal structure of N-terminal domain of human protein O-mannose… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8WZA1 · AlphaFold monomer V2.0 prediction for protein O-linked-mannose… · a predicted model of the same protein · chain A against A, TM-score 1.00
• Q14118 · AlphaFold monomer V2.0 prediction for dystroglycan (Q14118) · a predicted model of the same protein · chain C against A, TM-score 0.78

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 Q8WZA1
• Every structure of UniProt Q14118
• Elsewhere: RCSB PDB 5GGP · PDBe 5GGP · UniProt Q8WZA1 · UniProt Q14118