3QLQ

Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster

• PDB DOI: https://doi.org/10.2210/pdb3QLQ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia cathartica
• Mutation(s): No 


• Deposited: 2011-02-03 Released: 2012-02-08 
• Deposition Author(s): Sundberg, E.J., Bonsor, D.A., Trastoy, B., Chiara, J.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

Synthesis and Biophysical Study of Disassembling Nano hybrid Bioconjugates with a Cubic Octasilsesquioxane Core

Trastoy, B., Bonsor, D.A., Perez-Ojeda, M.E., Sundberg, E.J., Jimeno, M.L., Garcia-Fernandez, J.M., Chiara, J.L.

(2012) Adv Funct Mater 22: 3191-3201

• DOI: https://doi.org/10.1002/adfm.201200423

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: 103.59 kDa 
• Atom Count: 7,466 
• Modelled Residue Count: 939 
• 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 cathartica	Mutation(s): 0
UniProt
Find proteins for P81461 (Canavalia cathartica) Explore P81461  Go to UniProtKB:  P81461

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	G [auth A], J [auth B], M [auth C], P [auth D]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
MN	F [auth A], H [auth B], K [auth C], O [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	E [auth A], I [auth B], L [auth C], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.89	α = 90
b = 63.68	β = 93.23
c = 125.8	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Sundberg, E.J., Bonsor, D.A., Trastoy, B., Chiara, J.L.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-08-22
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary