› 5npr

X-ray diffraction
1.85Å resolution

The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor

Released:
DOI: 10.2210/pdb5npr/pdb
PDB entry 5npr coloured by chain, front view.
PDB entry 5npr coloured by chain, side view.
PDB entry 5npr coloured by chain, top view.
Source organisms:
Primary publication:
Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors.
Rafie K, Gorelik A, Trapannone R, Borodkin VS, van Aalten DMF
Bioconjug Chem 29 1834-1840 (2018)
PMID: 29723473

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127414 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit Chain: A
Molecule details ›
Chain: A
Length: 717 amino acids
Theoretical weight: 80.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O15294 (Residues: 325-1041; Coverage: 69%)
Gene name: OGT
Sequence domains:
bisubstrate inhibitor Chain: E
Molecule details ›
Chain: E
Length: 9 amino acids
Theoretical weight: 714 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand K 1 x K
Ligand 94T 1 x 94T
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: F222
Unit cell:
a: 138.038Å b: 150.951Å c: 200.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.205 0.236
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

7 review citations

Fueling the fire: emerging role of the hexosamine biosynthetic pathway in cancer.
Akella et al. (2019)
6 more

1 mention without citation

Radical-Pairing Interactions in a Molecular Switch Evidenced by Ion Mobility Spectrometry and Infrared Ion Spectroscopy.
Hanozin et al. (2021)