› 2drz

X-ray diffraction
2.19Å resolution

Crystal structure of the earthworm lectin C-terminal domain mutant in complex with lactose

Released:
DOI: 10.2210/pdb2drz/pdb
Model geometry
Fit model/data
PDB entry 2drz coloured by chain, front view.
PDB entry 2drz coloured by chain, side view.
PDB entry 2drz 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
Macromolecules (2 distinct):
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

Carbohydrate polymer : NEW Components: BGC, GAL
Carbohydrate polymer
1 bound ligand:
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 40.186Å b: 89.296Å c: 41.642Å
α: 90° β: 116.31° γ: 90°
R-values:
R R work R free
0.215 0.215 0.269
Expression system: Escherichia coli BL21(DE3)

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Citations

13 review citations

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