6F6Y

Crystal structure of galectin-3 CRD in complex with galactopentaose

• PDB DOI: https://doi.org/10.2210/pdb6F6Y/pdb

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


• Deposited: 2017-12-06 Released: 2018-12-19 
• Deposition Author(s): Hakansson, M., Andersen, M.C.F., Clausen, M.H., Logan, D.T.
• Funding Organization(s): Danish Council for Strategic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.153 
• R-Value Work: 0.116 
• R-Value Observed: 0.118 

Literature

Beta-(1-4)-d-galactans: synthesis and binding interactions with galectin-3

Andersen, M.C.F., Boos, I., Kinnaert, C., Awan, S.I., Pedersen, H.L., Kracun, S.K., Lanz, G., Rydahl, M.G., Kjaerulff, L., Hakansson, M., Kimbung, R., Logan, D.T., Gotfredsen, C.H., Willats, W.G.T., Clausen, M.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.08 kDa 
• Atom Count: 1,488 
• Modelled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	138	Homo sapiens	Mutation(s): 0  Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens) Explore P17931  Go to UniProtKB:  P17931
PHAROS:  P17931 GTEx:  ENSG00000131981

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G08806VI GlyCosmos:  G08806VI GlyGen:  G08806VI

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900113	B	4beta-beta-galactobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.153 
• R-Value Work: 0.116 
• R-Value Observed: 0.118 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.06	α = 90
b = 58.2	β = 90
c = 62.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Hakansson, M., Andersen, M.C.F., Clausen, M.H., Logan, D.T.

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Funding Organization	Location	Grant Number
Danish Council for Strategic Research	Denmark	GlycAct

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary