4RL7

Crystal structure of Human galectin-3 CRD in complex with lactose (pH 7.5, PEG6000)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The water network in galectin-3 ligand binding site guides inhibitor design

Su, J.Zhang, T.Wang, P.Liu, F.Tai, G.Zhou, Y.

(2015) ACTA BIOCHIM.BIOPHYS.SIN. --: --

  • DOI: 10.1093/abbs/gmu132
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Galectin-3 (Gal-3) which shows affinity of β-galactosides is a cancer-related protein. Thus, it is important to understand its ligand binding mechanism and then design its specific inhibitor. It was suggested that the positions of water molecules in ...

    Galectin-3 (Gal-3) which shows affinity of β-galactosides is a cancer-related protein. Thus, it is important to understand its ligand binding mechanism and then design its specific inhibitor. It was suggested that the positions of water molecules in Gal-3 ligand-binding site could be replaced by appropriate chemical groups of ideal inhibitors. However, the reported structures of Gal-3 carbohydrate recognition domain (CRD) complexed with lactose showed that the number of water molecules are different and the water positions are inconsistent in the ligand-binding site. This study reported four high-resolution (1.24-1.19 Å) structures of Gal-3 CRD complexed with lactose, and accurately located 12 conserved water molecules in the water network of Gal-3 CRD ligand-binding site by merging these structures. These water molecules either directly stabilize the binding of Gal-3 CRD and lactose, or hold the former water molecules at the right place. In particular, water molecule 4 (W4) which only coordinates with water molecule 5 (W5) and water molecule 6 (W6) plays a key role in stabilizing galactose residue. In addition, by three-dimensional alignment of the positions of all residues, 14 flexible parts of Gal-3 CRD were found to dynamically fluctuate in the crystalline environment.


    Organizational Affiliation

    School of Life Sciences, Northeast Normal University, Changchun 130024, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-3
A
144Homo 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKd: 93 - 230000 nM (100) BINDINGDB
LATIC50: 800000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.200α = 90.00
b = 57.800β = 90.00
c = 63.000γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-16 
  • Released Date: 2015-03-11 
  • Deposition Author(s): Su, J.Y.

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release