› 2xr5

X-ray diffraction
1.42Å resolution

Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.

Released:
DOI: 10.2210/pdb2xr5/pdb
PDB entry 2xr5 coloured by chain, front view.
PDB entry 2xr5 coloured by chain, side view.
PDB entry 2xr5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a glycomimetic ligand in the carbohydrate recognition domain of C-type lectin DC-SIGN. Structural requirements for selectivity and ligand design.
Thépaut M, Guzzi C, Sutkeviciute I, Sattin S, Ribeiro-Viana R, Varga N, Chabrol E, Rojo J, Bernardi A, Angulo J, Nieto PM, Fieschi F
J Am Chem Soc 135 2518-29 (2013)
PMID: 23360500

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-192443 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
CD209 antigen Chain: A
Molecule details ›
Chain: A
Length: 166 amino acids
Theoretical weight: 19.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NNX6 (Residues: 254-404; Coverage: 37%)
Gene names: CD209, CLEC4L
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A

Ligands and Environments

5 bound ligands:
Ligand MAN 1 x MAN
Ligand 07B 1 x 07B
Ligand ETA 1 x ETA
Ligand CA 3 x CA
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P43212
Unit cell:
a: 71.45Å b: 71.45Å c: 52.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.148 0.171
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Lipid-based mRNA vaccine delivery systems.
Midoux et al. (2015)
5 more

9 mentions without citation

Molecular Recognition in C-Type Lectins: The Cases of DC-SIGN, Langerin, MGL, and L-Sectin.
Valverde et al. (2020)
8 more