3NV3

Crystal structure of human galectin-9 C-terminal CRD in complex with biantennary oligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb3NV3/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-07 Released: 2010-09-22 
• Deposition Author(s): Yoshida, H., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.212 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.33 kDa 
• Atom Count: 1,272 
• Modelled Residue Count: 136 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin 9 short isoform variant	A	138	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00182 (Homo sapiens) Explore O00182  Go to UniProtKB:  O00182
PHAROS:  O00182 GTEx:  ENSG00000168961

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G28052FT GlyCosmos:  G28052FT GlyGen:  G28052FT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.212 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.003	α = 90
b = 71.003	β = 90
c = 49.741	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Yoshida, H., Kamitori, S.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary