1HJV

Crystal structure of hcgp-39 in complex with chitin tetramer

• PDB DOI: https://doi.org/10.2210/pdb1HJV/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-02-28 Released: 2003-03-11 
• Deposition Author(s): Houston, D.R., Recklies, A.D., Krupa, J.C., Van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.253 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 170.02 kDa 
• Atom Count: 12,296 
• Modelled Residue Count: 1,448 
• Deposited Residue Count: 1,448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE-3 LIKE PROTEIN 1	A, B, C, D	362	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens) Explore P36222  Go to UniProtKB:  P36222
PHAROS:  P36222 GTEx:  ENSG00000133048

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, L	4		N/A
Glycosylation Resources
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A], Q [auth B], U [auth C], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	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]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	E, G, I, K	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 108.645	α = 90
b = 123.321	β = 90
c = 135.486	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-11 
Deposition Author(s): Houston, D.R., Recklies, A.D., Krupa, J.C., Van Aalten, D.M.F.

Revision History  

• 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