6STN

Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N-Acetyl glucosamine

• PDB DOI: https://doi.org/10.2210/pdb6STN/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Arundo donax
• Mutation(s): No 


• Deposited: 2019-09-11 Released: 2021-07-14 
• Deposition Author(s): Perduca, M., Monaco, H.L., Bovi, M., Destefanis, L., Nadali, D., Fin, L., Carrizo, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

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: mass spectrometry

Macromolecule Content

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,512 
• Modelled Residue Count: 330 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arundo donax Lectin (ADL)	A, B	170	Arundo donax	Mutation(s): 0
UniProt
Find proteins for A0A0A9P802 (Arundo donax) Explore A0A0A9P802  Go to UniProtKB:  A0A0A9P802

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.55	α = 90
b = 127.55	β = 90
c = 45.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Perduca, M., Monaco, H.L., Bovi, M., Destefanis, L., Nadali, D., Fin, L., Carrizo, M.E.

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description