6A63

Placental protein 13/galectin-13 variant R53HH57R with Lactose

• PDB DOI: https://doi.org/10.2210/pdb6A63/pdb

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


• Deposited: 2018-06-26 Released: 2018-12-26 
• Deposition Author(s): Su, J.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.209 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

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: gel filtration

Macromolecule Content

• Total Structure Weight: 16.35 kDa 
• Atom Count: 1,264 
• Modelled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactoside-binding soluble lectin 13	A	138	Homo sapiens	Mutation(s): 2  Gene Names: LGALS13, PLAC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHV8 (Homo sapiens) Explore Q9UHV8  Go to UniProtKB:  Q9UHV8
PHAROS:  Q9UHV8 GTEx:  ENSG00000105198

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	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	B	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.209 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.934	α = 90
b = 92.964	β = 90
c = 50.521	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Su, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31500637

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary