Human ogt in complex with udp-5S-glcnac and substrate peptide (RBL2)

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 12% 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

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 · 977 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 965 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 567 Ų buried · 3 hydrogen bonds · protein-protein
• B–F · 433 Ų buried · 1 hydrogen bond · protein-protein
• A–E · 433 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 4XI9 · Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2) · 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
• Q08999 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 2 (Q08999) · a predicted model of the same protein · chain E against A, TM-score 0.58

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 Q08999
• Elsewhere: RCSB PDB 4XI9 · PDBe 4XI9 · UniProt O15294 · UniProt Q08999