6B94 | pdb_00006b94

Crystal structure of Human galectin-1 in complex with Lactulose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6B94

This is version 2.1 of the entry. See complete history

Literature

Lactulose as a novel template for anticancer drug development targeting galectins.

Kishor, C.Ross, R.L.Blanchard, H.

(2018) Chem Biol Drug Des 92: 1801-1808

  • DOI: https://doi.org/10.1111/cbdd.13348
  • Primary Citation Related Structures: 
    6B8K, 6B94

  • PubMed Abstract: 

    Galectins are carbohydrate binding proteins (lectins), which characteristically bind β-galactosides. Galectins play a role in tumour progression through involvement in proliferation, metastasis, angiogenesis, immune evasion and drug resistance. There is need for inhibitors (antagonists) that are specific for distinct galectins and that can interfere with galectin-carbohydrate interactions during cancer progression. Here, we propose that lactulose, a non-digestible galactose-fructose disaccharide, presents a novel inhibitor scaffold for design of inhibitors against galectins. Thermodynamic evaluation displays binding affinity of lactulose against the galectin-1 and galectin-3 carbohydrate recognition domain (CRD). Crystal structures of galectin-1 and galectin-3 in complex with lactulose reveal for the first time the molecular basis of the galectin-lactulose interactions. Molecular modelling was implemented to propose novel lactulose derivatives as potent anti-cancer agents.


  • Organizational Affiliation
    • Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.

Macromolecule Content 

  • Total Structure Weight: 30.8 kDa 
  • Atom Count: 2,325 
  • Modeled Residue Count: 268 
  • Deposited Residue Count: 268 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galectin-1
A, B
134Homo sapiensMutation(s): 0 
Gene Names: LGALS1
UniProt & NIH Common Fund Data Resources
Find proteins for P09382 (Homo sapiens)
Explore P09382 
Go to UniProtKB:  P09382
PHAROS:  P09382
GTEx:  ENSG00000100097 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09382
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G57229GY
GlyCosmos: G57229GY

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BME

Query on BME



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth B],
O [auth B],
P [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
M [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.23α = 90
b = 58.32β = 90
c = 111.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2025-04-02
    Changes: Data collection, Database references, Structure summary