› 2vmc

X-ray diffraction
1.9Å resolution

Structure of the complex of discoidin II from Dictyostelium discoideum with N-acetyl-galactosamine

Released:
DOI: 10.2210/pdb2vmc/pdb
PDB entry 2vmc coloured by chain, front view.
PDB entry 2vmc coloured by chain, side view.
PDB entry 2vmc coloured by chain, top view.
Source organism: Dictyostelium discoideum AX2
Primary publication:
Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.
Aragão KS, Satre M, Imberty A, Varrot A
Proteins 73 43-52 (2008)
PMID: 18384150

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-154660 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Discoidin-2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.61 KDa
Source organism: Dictyostelium discoideum AX2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42530 (Residues: 1-257; Coverage: 100%)
Gene names: DDB_G0292552, dscE
Sequence domains:
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand CL 2 x CL
Ligand CA 1 x CA
Ligand A2G 1 x A2G
Ligand NGA 1 x NGA
Ligand 1PG 2 x 1PG
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: R32
Unit cell:
a: 82.52Å b: 82.52Å c: 261.6Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.159 0.157 0.198
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses.
Dunn et al. (2017)
3 more

1 mention without citation

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