› 5ndf

X-ray diffraction
2.3Å resolution

Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation

Released:
DOI: 10.2210/pdb5ndf/pdb
PDB entry 5ndf coloured by chain, front view.
PDB entry 5ndf coloured by chain, side view.
PDB entry 5ndf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The small molecule luteolin inhibits N-acetyl-α-galactosaminyltransferases and reduces mucin-type O-glycosylation of amyloid precursor protein.
Liu F, Xu K, Xu Z, de Las Rivas M, Wang C, Li X, Lu J, Zhou Y, Delso I, Merino P, Hurtado-Guerrero R, Zhang Y, Wu F
J Biol Chem 292 21304-21319 (2017)
PMID: 29061849

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-galactosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-alpha-D-galactosaminyl)-L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171230 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Polypeptide N-acetylgalactosaminyltransferase 2 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 571 amino acids
Theoretical weight: 64.82 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q10471 (Residues: 1-571; Coverage: 100%)
Gene name: GALNT2
Sequence domains:
Structure domains: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Ligands and Environments

4 bound ligands:
Ligand MN 6 x MN
Ligand UDP 6 x UDP
Ligand EDO 10 x EDO
Ligand LU2 3 x LU2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P212121
Unit cell:
a: 116.98Å b: 123.111Å c: 248.152Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.213 0.251
Expression system: Komagataella pastoris

Quick links

Citations

3 review citations

Polypeptide GalNAc-Ts: from redundancy to specificity.
de Las Rivas et al. (2019)
2 more