5NF9

Structure of Galectin-3 CRD in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb5NF9/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-13 Released: 2017-06-21 
• Deposition Author(s): Ronin, C., Atmanene, C., Gautier, F.M., Djedaini Pilard, F., Teletchea, S., Ciesielski, F., Vivat Hannah, V., Grandjean, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.214 
• R-Value Work: 0.145 
• R-Value Observed: 0.148 

Literature

Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3.

Atmanene, C., Ronin, C., Teletchea, S., Gautier, F.M., Djedaini-Pilard, F., Ciesielski, F., Vivat, V., Grandjean, C.

(2017) Biochem Biophys Res Commun 489: 281-286

• PubMed: 28554839 
• DOI: https://doi.org/10.1016/j.bbrc.2017.05.150
• Primary Citation of Related Structures:  
  5NF7, 5NF9, 5NFA, 5NFB, 5NFC


• PubMed Abstract: 
  

  Combination of biophysical and structural techniques allowed characterizing and uncovering the mechanisms underlying increased binding affinity of lactosamine derivatives for galectin 3. In particular, complementing information gathered from X-ray crystallography, native mass spectrometry and isothermal microcalorimetry showed favorable enthalpic contribution of cation-π interaction between lactosamine aryl substitutions and arginine residues from the carbohydrate recognition domain, which resulted in two log increase in compound binding affinity. This incrementing strategy allowed individual contribution of galectin inhibitor moieties to be dissected. Altogether, our results suggest that core and substituents of these saccharide-based inhibitors can be optimized separately, providing valuable tools to study the role of galectins in diseases.

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Organizational Affiliation: 

NovAliX Structural Biology Bioparc, Bd Sébastien Brant, BP30170, F-67405 Illkirch Cedex, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 16.98 kDa 
• Atom Count: 1,284 
• Modelled Residue Count: 138 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	147	Homo sapiens	Mutation(s): 0  Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens) Explore P17931  Go to UniProtKB:  P17931
PHAROS:  P17931 GTEx:  ENSG00000131981

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8VW	B [auth A]	~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]-3-methoxy-benzamide C22 H32 N2 O12 SQNUIUJICOQQJY-NQSBSUMMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8VW	Binding MOAD:  5NF9	Kd: 4700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.214 
• R-Value Work: 0.145 
• R-Value Observed: 0.148 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.87	α = 90
b = 57.95	β = 90
c = 62.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Ronin, C., Atmanene, C., Gautier, F.M., Djedaini Pilard, F., Teletchea, S., Ciesielski, F., Vivat Hannah, V., Grandjean, C.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description