› 6h0b

X-ray diffraction
1.8Å resolution

Crystal structure of the human GalNAc-T4 in complex with UDP, manganese and the diglycopeptide 6.

Released:
DOI: 10.2210/pdb6h0b/pdb
PDB entry 6h0b coloured by chain, front view.
PDB entry 6h0b coloured by chain, side view.
PDB entry 6h0b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4.
de Las Rivas M, Paul Daniel EJ, Coelho H, Lira-Navarrete E, Raich L, Compañón I, Diniz A, Lagartera L, Jiménez-Barbero J, Clausen H, Rovira C, Marcelo F, Corzana F, Gerken TA, Hurtado-Guerrero R
ACS Cent Sci 4 1274-1290 (2018)
PMID: 30276263

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

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166797 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polypeptide N-acetylgalactosaminyltransferase 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 578 amino acids
Theoretical weight: 66.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8N4A0 (Residues: 1-578; Coverage: 100%)
Gene name: GALNT4
Sequence domains:
ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY Chain: F
Molecule details ›
Chain: F
Length: 16 amino acids
Theoretical weight: 1.2 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand EDO 36 x EDO
Ligand MN 1 x MN
Ligand UDP 1 x UDP
Ligand GOL 1 x GOL
Ligand NGA 2 x NGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P1
Unit cell:
a: 66.09Å b: 81.332Å c: 84.863Å
α: 65.55° β: 68.66° γ: 74.31°
R-values:
R R work R free
0.191 0.19 0.238
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

4 review citations

Mucins and the Microbiome.
Hansson GC. (2020)
3 more

4 mentions without citation

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