› 3wsr

X-ray diffraction
1.91Å resolution

Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin

Released:
DOI: 10.2210/pdb3wsr/pdb
PDB entry 3wsr coloured by chain, front view.
PDB entry 3wsr coloured by chain, side view.
PDB entry 3wsr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A platform of C-type lectin-like receptor CLEC-2 for binding O-glycosylated podoplanin and nonglycosylated rhodocytin.
Nagae M, Morita-Matsumoto K, Kato M, Kaneko MK, Kato Y, Yamaguchi Y
Structure 22 1711-1721 (2014)
PMID: 25458834

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183270 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
C-type lectin domain family 1 member B Chains: A, B
Molecule details ›
Chains: A, B
Length: 128 amino acids
Theoretical weight: 15.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9P126 (Residues: 96-221; Coverage: 55%)
Gene names: CLEC1B, CLEC2, UNQ721/PRO1384
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Podoplanin Chains: C, D
Molecule details ›
Chains: C, D
Length: 18 amino acids
Theoretical weight: 1.7 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q86YL7 (Residues: 38-54; Coverage: 12%)
Gene names: GP36, PDPN, PSEC0003, PSEC0025

Ligands and Environments

Carbohydrate polymer : NEW Components: A2G, GAL, SIA
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 54.369Å b: 51.194Å c: 54.099Å
α: 90° β: 112.77° γ: 90°
R-values:
R R work R free
0.219 0.217 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Functional significance of the platelet immune receptors GPVI and CLEC-2.
Rayes et al. (2019)
14 more

5 mentions without citation

Glycomimetics for the inhibition and modulation of lectins.
Leusmann et al. (2023)
4 more