4R9C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



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 (Shanghai) 

  • DOI: 10.1093/abbs/gmu132
  • Primary Citation of Related Structures:  
    4RL7, 4R9C, 4R9D, 4R9A, 4R9B

  • 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 zhouyf383@nenu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-3A144Homo sapiensMutation(s): 0 
Gene Names: LGALS3MAC2
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
NIH Common Fund Data Resources
PHAROS  P17931
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
B
2 N/A
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKd:  93   nM  BindingDB
LATIC50:  1000000   nM  BindingDB
LATKd:  222000   nM  BindingDB
LATIC50:  800000   nM  BindingDB
LATKd:  110000   nM  BindingDB
LATKd:  230000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.088α = 90
b = 57.552β = 90
c = 62.355γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-09-04 
  • Released Date: 2015-03-11 
  • Deposition Author(s): Su, J.Y.

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary