3WLU

Crystal Structure of human galectin-9 NCRD with Selenolactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


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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: 10.1016/j.bmc.2014.02.023

  • 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-methylselenob ...

    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

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan; Photon Science, SLAC Natl. Accelerator Laboratory Structure Science, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025-7015, USA; Department of Structural Biology, Stanford University, Beckman Center B105, 279 Campus Drive, Stanford, CA 94305-5126, USA.,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. Electronic address: hando@gifu-u.ac.jp.,Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-9
A, B, C, D
144Homo sapiensMutation(s): 0 
Gene Names: LGALS9
Find proteins for O00182 (Homo sapiens)
Go to Gene View: LGALS9
Go to UniProtKB:  O00182
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LSE
Query on LSE

Download SDF File 
Download CCD File 
A, B, C, D
2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside
C18 H36 O10 Se Si
DAHDBHYUNUXOAL-MUKCROHVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.732α = 90.00
b = 68.167β = 90.00
c = 224.156γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
ADSCdata collection
XDSdata reduction
REFMACrefinement
PHENIXmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release