› 5ggp

X-ray diffraction
1.6Å resolution

Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide

Released:
DOI: 10.2210/pdb5ggp/pdb
PDB entry 5ggp coloured by chain, front view.
PDB entry 5ggp coloured by chain, side view.
PDB entry 5ggp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.
Kuwabara N, Manya H, Yamada T, Tateno H, Kanagawa M, Kobayashi K, Akasaka-Manya K, Hirose Y, Mizuno M, Ikeguchi M, Toda T, Hirabayashi J, Senda T, Endo T, Kato R
Proc Natl Acad Sci U S A 113 9280-5 (2016)
PMID: 27493216

Function and Biology Details

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-171924 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 164 amino acids
Theoretical weight: 17.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WZA1 (Residues: 92-250; Coverage: 24%)
Gene names: MGAT1.2, POMGNT1, UNQ746/PRO1475
Sequence domains: Interleukin-like EMT inducer
Alpha-dystroglycan Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 amino acids
Theoretical weight: 927 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q14118 (Residues: 316-325; Coverage: 1%)
Gene name: DAG1

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
1 bound ligand:
Ligand NA 5 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 111.113Å b: 49.743Å c: 61.716Å
α: 90° β: 105.89° γ: 90°
R-values:
R R work R free
0.218 0.216 0.246
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Emerging structural insights into glycosyltransferase-mediated synthesis of glycans.
Moremen et al. (2019)
9 more

1 mention without citation

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.
Kuwabara et al. (2016)