› 6pi0

X-ray diffraction
2.09Å resolution

AgaD472N-Linear Blood group B type 2 trisaccharide complex structure

Released:
DOI: 10.2210/pdb6pi0/pdb
PDB entry 6pi0 coloured by chain, front view.
PDB entry 6pi0 coloured by chain, side view.
PDB entry 6pi0 coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Molecular analysis of an enigmatic Streptococcus pneumoniae virulence factor: The raffinose-family oligosaccharide utilization system.
Hobbs JK, Meier EPW, Pluvinage B, Mey MA, Boraston AB
J Biol Chem 294 17197-17208 (2019)
PMID: 31591266

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101481 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Alpha-galactosidase Chain: A
Molecule details ›
Chain: A
Length: 740 amino acids
Theoretical weight: 83.97 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H2URQ6 (Residues: 1-720; Coverage: 100%)
Gene names: SP_1898, aga
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, GLA
Carbohydrate polymer
3 bound ligands:
Ligand TLA 1 x TLA
Ligand EDO 7 x EDO
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-002
Spacegroup: I222
Unit cell:
a: 90.949Å b: 127.275Å c: 152.269Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1.
Lafond et al. (2020)
3 more