› 2dry

X-ray diffraction
1.8Å resolution

Crystal structure of the earthworm lectin C-terminal domain mutant

Released:
DOI: 10.2210/pdb2dry/pdb
PDB entry 2dry coloured by chain, front view.
PDB entry 2dry coloured by chain, side view.
PDB entry 2dry coloured by chain, top view.
Source organism: Lumbricus terrestris
Primary publication:
Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry.
Yabe R, Suzuki R, Kuno A, Fujimoto Z, Jigami Y, Hirabayashi J
J Biochem 141 389-99 (2007)
PMID: 17234683

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132139 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ricin B lectin domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 130 amino acids
Theoretical weight: 14.43 KDa
Source organism: Lumbricus terrestris
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O96048 (Residues: 131-260; Coverage: 50%)
Sequence domains: Ricin-type beta-trefoil lectin domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)

Ligands and Environments

2 bound ligands:
Ligand SO4 4 x SO4
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OTHER
Spacegroup: P21
Unit cell:
a: 40.151Å b: 89.562Å c: 41.67Å
α: 90° β: 116.39° γ: 90°
R-values:
R R work R free
0.234 0.234 0.263
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

13 review citations

Binding sugars: from natural lectins to synthetic receptors and engineered neolectins.
Arnaud et al. (2013)
12 more

1 mention without citation

Destruction-and-diffraction by X-ray free-electron laser.
Wang J. (2016)