› 2d5h

X-ray diffraction
2.8Å resolution

Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly

Released:
DOI: 10.2210/pdb2d5h/pdb
PDB entry 2d5h coloured by chain, front view.
PDB entry 2d5h coloured by chain, side view.
PDB entry 2d5h coloured by chain, top view.
Source organism: Glycine max
Primary publication:
Conservation and divergence on plant seed 11S globulins based on crystal structures.
Tandang-Silvas MR, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N
Biochim Biophys Acta 1804 1432-42 (2010)
PMID: 20215054

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137599 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycinin G5 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 493 amino acids
Theoretical weight: 55.75 KDa
Source organism: Glycine max
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04347 (Residues: 25-416, 417-516; Coverage: 100%)
Gene names: GY5, Glyma13g18450
Sequence domains: Cupin
Structure domains: Jelly Rolls

Ligands and Environments

2 bound ligands:
Ligand CO3 6 x CO3
Ligand MG 6 x MG
1 modified residue:
Ligand CSD 6 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: MACSCIENCE
Spacegroup: P21
Unit cell:
a: 89.378Å b: 223.738Å c: 88.66Å
α: 90° β: 119.85° γ: 90°
R-values:
R R work R free
0.248 0.248 0.325
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Cross-reactivity of peanut allergens.
Bublin et al. (2014)
9 more

2 mentions without citation

Structure of allergens and structure based epitope predictions.
Dall'antonia et al. (2014)
1 more