› 5vyg

X-ray diffraction
2.2Å resolution

Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide

Released:
DOI: 10.2210/pdb5vyg/pdb
PDB entry 5vyg coloured by chain, front view.
PDB entry 5vyg coloured by chain, side view.
PDB entry 5vyg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
O-Glycosylation modulates the stability of epidermal growth factor-like repeats and thereby regulates Notch trafficking.
Takeuchi H, Yu H, Hao H, Takeuchi M, Ito A, Li H, Haltiwanger RS
J Biol Chem 292 15964-15973 (2017)
PMID: 28729422

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133190 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Coagulation factor IXa light chain Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 50 amino acids
Theoretical weight: 5.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 92-130; Coverage: 9%)
Gene name: F9
Sequence domains: EGF-like domain
Structure domains: Laminin

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, XYS
Carbohydrate polymer
1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2
Unit cell:
a: 92.417Å b: 46.84Å c: 37.259Å
α: 90° β: 92.58° γ: 90°
R-values:
R R work R free
0.214 0.212 0.259
Expression system: Escherichia coli

Quick links

Citations

17 review citations

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

3 mentions without citation

Cryo-EM is uncovering the mechanism of eukaryotic protein N-glycosylation.
Bai et al. (2019)
2 more