1ONA

CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-3,6-DI-O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA-D-MANNOPYRANOSIDE

• PDB DOI: https://doi.org/10.2210/pdb1ONA/pdb

• Classification: PLANT LECTIN
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 1996-07-07 Released: 1997-09-17 
• Deposition Author(s): Bouckaert, J., Maes, D., Poortmans, F., Wyns, L., Loris, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.282 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 104.94 kDa 
• Atom Count: 7,368 
• Modelled Residue Count: 924 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONCANAVALIN A	A, B, C, D	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866  Go to UniProtKB:  P02866

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl alpha-D-mannopyranoside	E, F, G, H	3		N/A
Glycosylation Resources
GlyTouCan:  G27351BJ GlyCosmos:  G27351BJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	I [auth A], K [auth B], M [auth C], O [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	J [auth A], L [auth B], N [auth C], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.282 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.83	α = 90
b = 64.84	β = 93.87
c = 125.92	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-17 
Deposition Author(s): Bouckaert, J., Maes, D., Poortmans, F., Wyns, L., Loris, R.

Revision History  

• Version 1.0: 1997-09-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-02-17
  Changes: Derived calculations, Non-polymer description
• Version 1.4: 2018-04-18
  Changes: Data collection, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-09
  Changes: Database references, Refinement description, Structure summary