3QLQ

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin-A
A, B, C, D
237Canavalia catharticaMutation(s): 0 
UniProt
Find proteins for P81461 (Canavalia cathartica)
Explore P81461 
Go to UniProtKB:  P81461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81461
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
O [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
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 = 59.89α = 90
b = 63.68β = 93.23
c = 125.8γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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