6EYM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    6F2Q, 6EXY, 6EYM

  • 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 been based on mono- or disaccharide cores closely resembling natural ligands ...

    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

    Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-3A138Homo sapiensMutation(s): 0 
Gene Names: LGALS3MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
PHAROS:  P17931
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84224TW
GlyCosmos:  G84224TW
GlyGen:  G84224TW
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LAT BindingDB:  6EYM Kd: min: 93, max: 2.30e+5 (nM) from 4 assay(s)
IC50: min: 8.00e+5, max: 1.00e+6 (nM) from 2 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004
Bbeta-lactoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.01α = 90
b = 58.36β = 90
c = 63.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
Mantiddata reduction
XPREPdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Spallation SourceSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary