Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.33 kDa 
• Atom Count: 3647 
• Modelled Residue Count: 365 
• Deposited Residue Count: 371 
• Unique protein chains: 1

4P8V

The crystal structures of YKL-39 in the presence of chitooligosaccharides (GlcNAc2) were solved to resolutions of 1.5 angstrom

• DOI: 10.2210/pdb4P8V/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-04-01 Released: 2014-12-03 
• Deposition Author(s): Suginta, W., Ranok, A., Robinson, R.C., Wongsantichon, J.
• Funding Organization(s): The Higher Education Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

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

• PubMed: 25477513 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 2	A	371	Homo sapiens	Mutation(s): 2  Gene Names: CHI3L2
Find proteins for Q15782 (Homo sapiens) Explore Q15782  Go to UniProtKB:  Q15782
NIH Common Fund Data Resources
PHAROS:  Q15782 GTEx:  ENSG00000064886

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.682	α = 90
b = 70.682	β = 90
c = 140.255	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-04-01 
• Released Date: 2014-12-03 
Deposition Author(s): Suginta, W., Ranok, A., Robinson, R.C., Wongsantichon, J.

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Funding Organization	Location	Grant Number
The Higher Education Commission	Thailand	CHE500307

Revision History  

• 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, Source and taxonomy, Structure summary