4YM3

Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose

• PDB DOI: https://doi.org/10.2210/pdb4YM3/pdb

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


• Deposited: 2015-03-06 Released: 2015-07-01 
• Deposition Author(s): Bum-Erdene, K., Blanchard, H.
• Funding Organization(s): Cancer Council Queensland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.22 kDa 
• Atom Count: 4,784 
• Modelled Residue Count: 557 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-4	A, B, C, D	153	Homo sapiens	Mutation(s): 0  Gene Names: LGALS4
UniProt & NIH Common Fund Data Resources
Find proteins for P56470 (Homo sapiens) Explore P56470  Go to UniProtKB:  P56470
PHAROS:  P56470 GTEx:  ENSG00000171747

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	E, F, G, H	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.533	α = 90
b = 130.185	β = 96.91
c = 45.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Bum-Erdene, K., Blanchard, H.

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Funding Organization	Location	Grant Number
Cancer Council Queensland	Australia	1043716

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• 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: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary