2Q3N

Agglutinin from Abrus Precatorius (APA-I)

• PDB DOI: https://doi.org/10.2210/pdb2Q3N/pdb
• Entry: 2Q3N supersedes: 2AMZ

• Classification: PLANT PROTEIN
• Organism(s): Abrus precatorius
• Mutation(s): No 


• Deposited: 2007-05-30 Released: 2007-06-26 
• Deposition Author(s): Bagaria, A., Surendranath, K., Ramagopal, U.A., Ramakumar, S., Karande, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.58 kDa 
• Atom Count: 4,028 
• Modelled Residue Count: 508 
• Deposited Residue Count: 527 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin-1 A chain	A	260	Abrus precatorius	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for Q9M6E9 (Abrus precatorius) Explore Q9M6E9  Go to UniProtKB:  Q9M6E9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglutinin-1 B chain	B	267	Abrus precatorius	Mutation(s): 0
UniProt
Find proteins for Q9M6E9 (Abrus precatorius) Explore Q9M6E9  Go to UniProtKB:  Q9M6E9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth B], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.255 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.122	α = 90
b = 141.122	β = 90
c = 105.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Bagaria, A., Surendranath, K., Ramagopal, U.A., Ramakumar, S., Karande, A.A.
• This entry supersedes: 2AMZ

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary