Crystal structure of hcgp-39 in complex with chitin tetramer

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Structure and Ligand-Induced Conformational Change of the 39-kDa Glycoprotein from Human Articular Chondrocytes.

Houston, D.R.Recklies, A.D.Krupa, J.C.Van Aalten, D.M.F.

(2003) J Biol Chem 278: 30206

  • DOI: https://doi.org/10.1074/jbc.M303371200
  • Primary Citation of Related Structures:  
    1HJV, 1HJW, 1HJX

  • PubMed Abstract: 

    The 39-kDa human cartilage glycoprotein (HCGP39), a member of a novel family of chitinase-like lectins (Chilectins), is overexpressed in articular chondrocytes and certain cancers. Proposed functions of this protein include a role in connective tissue remodeling and defense against pathogens. Similar to other Chi-lectins, HCGP39 promotes the growth of connective tissue cells. The ability of HCGP39 to activate cytoplasmic signaling pathways suggests the presence of a ligand for this protein at the cell surface. There is currently no information regarding the identity of any physiological or pathological ligands of the Chi-lectins or the nature of the protein-ligand interaction. Here, we show that HCGP39 is able to bind chitooligosaccharides with micromolar affinity. Crystal structures of the native protein and a complex with GlcNAc8 show that the ligand is bound in identical fashion to family 18 chitinases. However, unlike the chitinases, binding of the oligosaccharide ligand to HCGP39 induces a large conformational change. Thus, HCGP39 could be a lectin that binds chitin-like oligosaccharide ligands and possibly plays a role in innate responses to chitinous pathogens, such as fungi and nematodes.

  • Organizational Affiliation

    Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
362Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens)
Explore P36222 
Go to UniProtKB:  P36222
GTEx:  ENSG00000133048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36222
Glycosylation Sites: 1Go to GlyGen: P36222-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, G, I, K
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
F, H, J, L
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
U [auth C],
Y [auth D]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
N [auth A]
O [auth A]
P [auth A]
AA [auth D],
BA [auth D],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth C],
Z [auth D]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.645α = 90
b = 123.321β = 90
c = 135.486γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary