Human O-glcnac transferase (ogt) in complex with udp-5SGLCNAC and substrate peptide

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).

Ligands and binding sites

• 12V · (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S, 4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3, 4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
• SO4 · Sulfate ion · ion · 4 copies · chains A, E, B, F, C, G, D, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• B–C · 948 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 940 Ų buried · 9 hydrogen bonds · protein-protein
• C–G · 677 Ų buried · 4 hydrogen bonds · protein-protein
• D–H · 671 Ų buried · 4 hydrogen bonds · protein-protein
• B–F · 671 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

• 4AY6 · Human O-GlcNAc transferase (OGT) in complex with UDP-5SGlcNAc and substrate peptide · the same entry in another collection · chain H against H, TM-score 1.00
• O15294 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.96
• Q15750 · AlphaFold monomer V2.0 prediction for TGF-beta-activated kinase 1 and MAP3K7-binding… · a predicted model of the same protein · chain E against A, TM-score 0.37

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 O15294
• Every structure of UniProt Q15750
• Elsewhere: RCSB PDB 4AY6 · PDBe 4AY6 · UniProt O15294 · UniProt Q15750