5VWG | pdb_00005vwg

Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside

• PDB DOI: https://doi.org/10.2210/pdb5VWG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-21 Released: 2018-05-23 
• Deposition Author(s): Bohari, M.H., Yu, X., Blanchard, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside

Blanchard, H., Yu, X., Bohari, M.H.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 17.79 kDa 
• Atom Count: 1,309 
• Modeled Residue Count: 147 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-8	A	155	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9QG	B [auth A]	methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactopyranoside C10 H18 O8 PXMURYZLIUEKLA-BEESJRNYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.777	α = 90
b = 50.145	β = 90
c = 80.695	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Bohari, M.H., Yu, X., Blanchard, H.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-23
  Changes: Structure summary