2YY1 | pdb_00002yy1

Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine

• PDB DOI: https://doi.org/10.2210/pdb2YY1/pdb

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


• Deposited: 2007-04-27 Released: 2008-04-29 
• Deposition Author(s): Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.244 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine

Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.61 kDa 
• Atom Count: 1,194 
• Modeled Residue Count: 141 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-9	A	160	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-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G79333MY GlyCosmos:  G79333MY GlyGen:  G79333MY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900019	B	N-acetyl-alpha-lactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.244 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.407	α = 90
b = 47.407	β = 90
c = 121.609	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-29
  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, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2020-09-09
  Changes: Database references, Structure summary
• Version 2.2: 2024-03-13
  Changes: Data collection, Database references