3WLU

Crystal Structure of human galectin-9 NCRD with Selenolactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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This is version 1.1 of the entry. See complete history


Literature

Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing

Suzuki, T.Makyio, H.Ando, H.Komura, N.Menjo, M.Yamada, Y.Imamura, A.Ishida, H.Wakatsuki, S.Kato, R.Kiso, M.

(2014) Bioorg Med Chem 22: 2090-2101

  • DOI: https://doi.org/10.1016/j.bmc.2014.02.023
  • Primary Citation of Related Structures:  
    3WLU

  • PubMed Abstract: 

    Seleno-lactoses have been successfully synthesized as candidates for mimicking carbohydrate ligands for human galectin-9 N-terminal carbohydrate recognition domain (NCRD). Selenium was introduced into the mono- or di-saccharides using p-methylselenobenzoic anhydride (Tol2Se) as a novel selenating reagent. The TolSe-substituted monosaccharides were converted into selenoglycosyl donors or acceptors, which were reacted with coupling partners to afford seleno-lactoses. The seleno-lactoses were converted to the target compounds. The structure of human galectin-9 NCRD co-crystallized with 6-MeSe-lactose was determined with single/multi-wavelength anomalous dispersion (SAD/MAD) phasing and was similar to that of the co-crystal with natural lactose.


  • Organizational Affiliation

    Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-9
A, B, C, D
144Homo sapiensMutation(s): 0 
Gene Names: LGALS9
UniProt & NIH Common Fund Data Resources
Find proteins for O00182 (Homo sapiens)
Explore O00182 
Go to UniProtKB:  O00182
PHAROS:  O00182
GTEx:  ENSG00000168961 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00182
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.732α = 90
b = 68.167β = 90
c = 224.156γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations