Human ogt in complex with udp-5S-glcnac and substrate peptide (RB2L)

Structure

x-ray diffraction · 2 distinct chains · 51% 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 · chains A, C
• PO4 · Phosphate ion · ion · 2 copies · chains A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 438 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5C1D · Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L) · the same entry in another collection · chain A against A, 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 0.98
• Q08999 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 2 (Q08999) · a predicted model of the same protein · chain C against A, TM-score 0.45

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 5C1D · PDBe 5C1D · UniProt O15294 · UniProt Q08999