› 5ava

X-ray diffraction
3Å resolution

Crystal structure of PHA-E lectin in complex with bisected glycan

Released:
DOI: 10.2210/pdb5ava/pdb
PDB entry 5ava coloured by chain, front view.
PDB entry 5ava coloured by chain, side view.
PDB entry 5ava coloured by chain, top view.
Source organism: Phaseolus vulgaris
Primary publication:
Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins.
Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y
OpenAccess logo Sci Rep 6 22973 (2016)
PMID: 26971576

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138409 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Erythroagglutinating phytohemagglutinin Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 275 amino acids
Theoretical weight: 29.82 KDa
Source organism: Phaseolus vulgaris
UniProt:
  • Canonical: P05088 (Residues: 1-275; Coverage: 100%)
Gene name: DLEC1
Sequence domains: Legume lectin domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL
Carbohydrate polymer
2 bound ligands:
Ligand MN 8 x MN
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 95.21Å b: 122.838Å c: 97.664Å
α: 90° β: 90.66° γ: 90°
R-values:
R R work R free
0.231 0.229 0.274

Quick links

Citations

7 review citations

Enzymes for N-Glycan Branching and Their Genetic and Nongenetic Regulation in Cancer.
Kizuka et al. (2016)
6 more

9 mentions without citation

Are Dietary Lectins Relevant Allergens in Plant Food Allergy?
Barre et al. (2020)
8 more