› 5fv9

X-ray diffraction
2.07Å resolution

Crystal structure of GalNAc-T2 in complex with compound 16d

Released:
DOI: 10.2210/pdb5fv9/pdb
PDB entry 5fv9 coloured by chain, front view.
PDB entry 5fv9 coloured by chain, side view.
PDB entry 5fv9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates.
Ghirardello M, de Las Rivas M, Lacetera A, Delso I, Lira-Navarrete E, Tejero T, Martín-Santamaría S, Hurtado-Guerrero R, Merino P
Chemistry 22 7215-24 (2016)
PMID: 27071848

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

5 bound ligands:
Ligand UDP 6 x UDP
Ligand MN 6 x MN
Ligand EDO 14 x EDO
Ligand GOL 5 x GOL
Ligand Y6W 3 x Y6W
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 116.493Å b: 121.748Å c: 250.155Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.19 0.247
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