The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc6) were solved to resolutions of 2.48 angstrom

Experimental Data Snapshot

  • Resolution: 2.48 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39).

Ranok, A.Wongsantichon, J.Robinson, R.C.Suginta, W.

(2015) J Biol Chem 290: 2617-2629

  • DOI: https://doi.org/10.1074/jbc.M114.588905
  • Primary Citation of Related Structures:  
    4P8U, 4P8V, 4P8W, 4P8X

  • PubMed Abstract: 

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.

  • Organizational Affiliation

    From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase-3-like protein 2371Homo sapiensMutation(s): 2 
Gene Names: CHI3L2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15782 (Homo sapiens)
Explore Q15782 
Go to UniProtKB:  Q15782
PHAROS:  Q15782
GTEx:  ENSG00000064886 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15782
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G36414FS
GlyCosmos:  G36414FS
GlyGen:  G36414FS
Experimental Data & Validation

Experimental Data

  • Resolution: 2.48 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.207α = 90
b = 71.207β = 90
c = 141.023γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The Office of the Higher Education CommissionThailandCHE500307

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2015-02-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary