› 2wn3

X-ray diffraction
1.59Å resolution

Crystal structure of Discoidin I from Dictyostelium discoideum in complex with the disaccharide GalNAc beta 1-3 galactose, at 1.6 A resolution.

Released:
DOI: 10.2210/pdb2wn3/pdb
PDB entry 2wn3 coloured by chain, front view.
PDB entry 2wn3 coloured by chain, side view.
PDB entry 2wn3 coloured by chain, top view.
Source organism: Dictyostelium discoideum AX2
Primary publication:
Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II.
Mathieu SV, Aragão KS, Imberty A, Varrot A
J Mol Biol 400 540-54 (2010)
PMID: 20580724

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136334 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Discoidin-1 subunit A Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 254 amino acids
Theoretical weight: 28.35 KDa
Source organism: Dictyostelium discoideum AX2
Expression system: Escherichia coli
UniProt:
  • Canonical: P02886 (Residues: 1-253; Coverage: 100%)
Gene names: DDB_G0273063, DDB_G0273919, dscA-1, dscA-2
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, NGA
Carbohydrate polymer
4 bound ligands:
Ligand CA 3 x CA
Ligand SO4 3 x SO4
Ligand 1PG 1 x 1PG
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2221
Unit cell:
a: 72.58Å b: 274Å c: 85.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.152 0.18
Expression system: Escherichia coli

Quick links

Citations

8 review citations

X-linked juvenile retinoschisis: clinical diagnosis, genetic analysis, and molecular mechanisms.
Molday et al. (2012)
7 more

3 mentions without citation

Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II.
Mathieu et al. (2010)
2 more