› 2vme

X-ray diffraction
2.45Å resolution

Structure of the wild-type discoidin II from Dictyostelium discoideum

Released:
DOI: 10.2210/pdb2vme/pdb
PDB entry 2vme coloured by chain, front view.
PDB entry 2vme coloured by chain, side view.
PDB entry 2vme 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 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 257 amino acids
Theoretical weight: 28.69 KDa
Source organism: Dictyostelium discoideum AX2
UniProt:
  • Canonical: P42530 (Residues: 1-257; Coverage: 100%)
Gene names: DDB_G0292552, dscE
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand CA 6 x CA
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand GOL 15 x GOL
Ligand PG4 1 x PG4
1 modified residue:
Ligand HIP 6 x HIP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 287.885Å b: 56.281Å c: 123.674Å
α: 90° β: 109.1° γ: 90°
R-values:
R R work R free
0.184 0.181 0.238

Quick links

Citations

3 review citations

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

3 mentions without citation

The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins.
Kalagiri et al. (2021)
2 more