5D5G

Structure of colocasia esculenta agglutinin

• PDB DOI: https://doi.org/10.2210/pdb5D5G/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Colocasia esculenta
• Mutation(s): No 


• Deposited: 2015-08-10 Released: 2015-09-02 
• Deposition Author(s): Biswas, H., Chattopadhyaya, R.
• Funding Organization(s): Department of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.427 
• R-Value Work: 0.344 
• R-Value Observed: 0.345 

Literature

Crystal structure Colocasia esculenta tuber agglutinin at 1.74A resolution and its quaternary interactions

Chattopadhyaya, R., Biswas, H., Sarkar, A.

(2017) J Glycobiol 6: 1000126-1000126

• DOI: https://doi.org/10.4172/2168-958X.1000126

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 49.32 kDa 
• Atom Count: 3,577 
• Modelled Residue Count: 439 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	A, C	109	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27  Go to UniProtKB:  R9RL27

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tuber agglutinin	B, D	111	Colocasia esculenta	Mutation(s): 0
UniProt
Find proteins for R9RL27 (Colocasia esculenta) Explore R9RL27  Go to UniProtKB:  R9RL27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.427 
• R-Value Work: 0.344 
• R-Value Observed: 0.345 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.012	α = 90
b = 47.198	β = 90
c = 82.251	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Biswas, H., Chattopadhyaya, R.

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Funding Organization	Location	Grant Number
Department of Science and Technology	India	none

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description