› 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 entry 4p8w coloured by chain, front view.
PDB entry 4p8w coloured by chain, side view.
PDB entry 4p8w coloured by chain, top view.
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 290 2617-29 (2015)
PMID: 25477513

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172395 (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%)
Gene name: CHI3L2
Sequence domains: Glycosyl hydrolases family 18
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NDG, NAG
Carbohydrate polymer
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

6 review citations

Live and let die: insights into pseudoenzyme mechanisms from structure.
Murphy et al. (2017)
5 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)