› 2d7r

X-ray diffraction
2.8Å resolution

Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on lectin domain

Released:
DOI: 10.2210/pdb2d7r/pdb
PDB entry 2d7r coloured by chain, front view.
PDB entry 2d7r coloured by chain, side view.
PDB entry 2d7r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10).
Kubota T, Shiba T, Sugioka S, Furukawa S, Sawaki H, Kato R, Wakatsuki S, Narimatsu H
J Mol Biol 359 708-27 (2006)
PMID: 16650853

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183154 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Polypeptide N-acetylgalactosaminyltransferase 10 Chain: A
Molecule details ›
Chain: A
Length: 570 amino acids
Theoretical weight: 65.47 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q86SR1 (Residues: 40-603; Coverage: 94%)
Gene name: GALNT10
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand NAG 2 x NAG
Ligand NGA 1 x NGA
Ligand MN 1 x MN
Ligand UDP 1 x UDP
Ligand SER 1 x SER
Ligand A2G 1 x A2G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2221
Unit cell:
a: 80.195Å b: 132.812Å c: 138.953Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.229 0.298
Expression system: Komagataella pastoris

Quick links

Citations

13 review citations

Glycosyltransferases: structures, functions, and mechanisms.
Lairson et al. (2008)
12 more

4 mentions without citation

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