3VKO

Galectin-8 N-terminal domain in complex with sialyllactosamine

• PDB DOI: https://doi.org/10.2210/pdb3VKO/pdb

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


• Deposited: 2011-11-18 Released: 2012-09-12 
• Deposition Author(s): Kamitori, S., Yoshida, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 

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)

Macromolecule Content

• Total Structure Weight: 36.12 kDa 
• Atom Count: 2,694 
• Modelled Residue Count: 294 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-8	A, B	153	Homo sapiens	Mutation(s): 0  Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens) Explore O00214  Go to UniProtKB:  O00214
PHAROS:  O00214 GTEx:  ENSG00000116977

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	C, D	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 61.5	β = 90
c = 84.07	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Kamitori, S., Yoshida, H.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary