› 6s24

X-ray diffraction
2.12Å resolution

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3

Released:
DOI: 10.2210/pdb6s24/pdb
PDB entry 6s24 coloured by chain, front view.
PDB entry 6s24 coloured by chain, side view.
PDB entry 6s24 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.
de Las Rivas M, Paul Daniel EJ, Narimatsu Y, Compañón I, Kato K, Hermosilla P, Thureau A, Ceballos-Laita L, Coelho H, Bernadó P, Marcelo F, Hansen L, Maeda R, Lostao A, Corzana F, Clausen H, Gerken TA, Hurtado-Guerrero R
Nat Chem Biol 16 351-360 (2020)
PMID: 31932717

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:
  • 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-124715 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polypeptide N-acetylgalactosaminyltransferase 3 Chain: A
Molecule details ›
Chain: A
Length: 631 amino acids
Theoretical weight: 72.37 KDa
Source organism: Taeniopygia guttata
Expression system: Komagataella pastoris
UniProt:
  • Canonical: H0ZAB5 (Residues: 1-540, 541-616; Coverage: 100%)
Gene name: GALNT3
Sequence domains:
ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO Chain: F
Molecule details ›
Chain: F
Length: 14 amino acids
Theoretical weight: 1.09 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand TAM 1 x TAM
Ligand PO4 16 x PO4
Ligand UDP 1 x UDP
Ligand MN 1 x MN
Ligand NAG 1 x NAG
Ligand NGA 1 x NGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 50.655Å b: 104.661Å c: 143.186Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.237
Expression systems:
  • Komagataella pastoris
  • Not provided

Quick links

Citations

12 review citations

Global view of human protein glycosylation pathways and functions.
Schjoldager et al. (2020)
11 more

4 mentions without citation

Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.
de Las Rivas et al. (2020)
3 more