1QGL

Room temperature structure of concanavalin A complexed to bivalent ligand

• PDB DOI: https://doi.org/10.2210/pdb1QGL/pdb

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


• Deposited: 1999-04-30 Released: 1999-05-20 
• Deposition Author(s): Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.200 
• R-Value Work: 0.176 

Literature

On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A

Dimick, S.M., Powell, S.C., Mcmahon, S.A., Moothoo, D.N., Naismith, J.H., Toone, E.J.

(1999) J Am Chem Soc 121: 10286-10296

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.21 kDa 
• Atom Count: 3,747 
• Modelled Residue Count: 474 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJT	E [auth A]	1,3-DI(N-PROPYLOXY-A-MANNOPYRANOSYL)-CARBOMYL 5-METHYAZIDO-BENZENE C27 H41 N5 O14 GKRIMQPDERYOML-LHMXEDMUSA-N
SIN	H [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.200 
• R-Value Work: 0.176 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.1	α = 90
b = 127.4	β = 90
c = 118.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-20 
Deposition Author(s): Naismith, J.H.

Revision History  

• Version 1.0: 1999-05-20
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Advisory, Data collection
• Version 1.4: 2023-08-16
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description