6F83 | pdb_00006f83

Crystal Structure of Human Galectin-1 in Complex With Thienyl-1,2, 3-triazolyl Thiodigalactoside Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6F83/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-12-12 Released: 2019-01-30 
• Deposition Author(s): Collins, P.M., Blanchard, H.
• Funding Organization(s): Cancer Council Queensland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Aromatic heterocycle galectin-1 interactions for selective single-digit nM affinity ligands

Peterson, A., Collins, P.M., Kahl-Knutsson, B., Zetterberg, F.R., Blanchard, H., Leffler, H., Nilsson, U.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 31.21 kDa 
• Atom Count: 2,315 
• Modeled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B	134	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5KT (Subject of Investigation/LOI)	C [auth A], D [auth B]	3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside C24 H28 N6 O8 S3 OYKAQKLJBYMZSV-VLLPDFJVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.447	α = 90
b = 58.689	β = 90
c = 112.353	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Collins, P.M., Blanchard, H.

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Funding Organization	Location	Grant Number
Cancer Council Queensland	Australia	ID1080845

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary