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.,School of Life Sciences, Northeast Normal University, Changchun 130024, China zhouyf383@nenu.edu.cn.




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