6EYM

Neutron crystal structure of perdeuterated galectin-3C in complex with lactose


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design.

Manzoni, F.Wallerstein, J.Schrader, T.E.Ostermann, A.Coates, L.Akke, M.Blakeley, M.P.Oksanen, E.Logan, D.T.

(2018) J. Med. Chem. 61: 4412-4420

  • DOI: 10.1021/acs.jmedchem.8b00081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The medically important drug target galectin-3 binds galactose-containing moieties on glycoproteins through an intricate pattern of hydrogen bonds to a largely polar surface-exposed binding site. All successful inhibitors of galectin-3 to date have b ...

    The medically important drug target galectin-3 binds galactose-containing moieties on glycoproteins through an intricate pattern of hydrogen bonds to a largely polar surface-exposed binding site. All successful inhibitors of galectin-3 to date have been based on mono- or disaccharide cores closely resembling natural ligands. A detailed understanding of the H-bonding networks in these natural ligands will provide an improved foundation for the design of novel inhibitors. Neutron crystallography is an ideal technique to reveal the geometry of hydrogen bonds because the positions of hydrogen atoms are directly detected rather than being inferred from the positions of heavier atoms as in X-ray crystallography. We present three neutron crystal structures of the C-terminal carbohydrate recognition domain of galectin-3: the ligand-free form and the complexes with the natural substrate lactose and with glycerol, which mimics important interactions made by lactose. The neutron crystal structures reveal unambiguously the exquisite fine-tuning of the hydrogen bonding pattern in the binding site to the natural disaccharide ligand. The ligand-free structure shows that most of these hydrogen bonds are preserved even when the polar groups of the ligand are replaced by water molecules. The protonation states of all histidine residues in the protein are also revealed and correlate well with NMR observations. The structures give a solid starting point for molecular dynamics simulations and computational estimates of ligand binding affinity that will inform future drug design.


    Related Citations: 
    • Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C.
      Manzoni, F.,Saraboji, K.,Sprenger, J.,Kumar, R.,Noresson, A.L.,Nilsson, U.J.,Leffler, H.,Fisher, S.Z.,Schrader, T.E.,Ostermann, A.,Coates, L.,Blakeley, M.P.,Oksanen, E.,Logan, D.T.
      (2016) Acta Crystallogr D Struct Biol 72: 1194


    Organizational Affiliation

    Institut Laue-Langevin , 71 avenue des Martyrs , 38000 Grenoble , France.,Instrument Division , European Spallation Source ERIC , Box 176, S-221 00 Lund , Sweden.,Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden.,Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstrasse 1 , 85747 Garching , Germany.,Department of Biophysical Chemistry , Lund University , S-221 00 Lund , Sweden.,Heinz Maier-Leibnitz Zentrum (MLZ) , Technische Universität München , Lichtenbergstrasse 1 , 85748 Garching , Germany.,Neutron Scattering Division , Oak Ridge National Laboratory , 1 Bethel Valley Road , Oak Ridge , Tennessee 37831 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-3
A
138Homo sapiensMutation(s): 0 
Gene Names: LGALS3 (MAC2)
Find proteins for P17931 (Homo sapiens)
Go to Gene View: LGALS3
Go to UniProtKB:  P17931
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAT
Query on LAT

Download SDF File 
Download CCD File 
A
BETA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-DCSYEGIMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.010α = 90.00
b = 58.360β = 90.00
c = 63.820γ = 90.00
Software Package:
Software NamePurpose
Mantiddata reduction
PHENIXrefinement
LAUEGENdata reduction
LSCALEdata scaling
PHENIXphasing
SCALAdata scaling
XPREPdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Spallation SourceSweden--

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Experimental preparation