› 4p8w

X-ray diffraction
1.87Å resolution

The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc4) were solved to resolutions of 1.9 angstrom

Released:
DOI: 10.2210/pdb4p8w/pdb
PDB 4p8w coloured by chain and viewed from the front.
PDB 4p8w coloured by chain and viewed from the side.
PDB 4p8w coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).
Ranok A, Wongsantichon J, Robinson RC, Suginta W
J. Biol. Chem. (2014)
PMID: 25477513

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Chitinase-3-like protein 2 Chain: A
Molecule details ›
Chain: A
Length: 371 amino acids
Theoretical weight: 41.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15782 (Residues: 27-390; Coverage: 100%)
  • Best match: Q15782-6 (Residues: 17-380)
Gene name: CHI3L2
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NDG, NAG
Ligand NDG 1 x NDG
Ligand NAG 3 x NAG
1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P41212
Unit cell:
a: 71.354Å b: 71.354Å c: 140.528Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Structural insights into the mechanisms and specificities of IgG-active endoglycosidases.
Du et al. (2020)
4 more

1 mention without citation

Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).
Ranok et al. (2015)