1AZD | pdb_00001azd

CONCANAVALIN FROM CANAVALIA BRASILIENSIS

• PDB DOI: https://doi.org/10.2210/pdb1AZD/pdb

• Classification: LECTIN
• Organism(s): Canavalia brasiliensis
• Mutation(s): No 


• Deposited: 1997-11-16 Released: 1998-04-29 
• Deposition Author(s): Sanz-Aparicio, J., Hermoso, J., Grangeiro, T.B., Calvete, J.J., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of Canavalia brasiliensis lectin suggests a correlation between its quaternary conformation and its distinct biological properties from Concanavalin A.

Sanz-Aparicio, J., Hermoso, J., Grangeiro, T.B., Calvete, J.J., Cavada, B.S.

(1997) FEBS Lett 405: 114-118

• PubMed: 9094437 
• DOI: https://doi.org/10.1016/s0014-5793(97)00137-3
• Primary Citation Related Structures: 
  1AZD


• PubMed Abstract: 
  

  Canavalia brasiliensis lectin was isolated from the seeds of a Brazilian autochthonous Leguminosae plant. Despite extensive amino acid sequence similarity with Concanavalin A, C. brasiliensis lectin exerts in vitro and in vivo cellular effects that are markedly different from those displayed by Concanavalin A. We have solved the crystal structure of the C. brasiliensis lectin at 3.0 A resolution. The three-dimensional structure of the lectin monomer can be superimposed onto that of Concanavalin A with a root-mean-square deviation for all C alpha atoms of 0.65 A. However, this parameter is 0.84 and 1.62 A when the C. brasiliensis lectin dimer and tetramer, respectively, are compared with the same structures of Concanavalin A. We suggest that these differences in quaternary structure may account for the different biological properties of these two highly related Leguminosae lectins.

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Organizational Affiliation: 
• Instituto de Química-Física Rocasolano CSIC, Departamento de Cristalografía, Madrid, Spain.

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: 102.75 kDa 
• Atom Count: 7,579 
• Modeled Residue Count: 948 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONBR	A, B, C, D	237	Canavalia brasiliensis	Mutation(s): 0
UniProt
Find proteins for P55915 (Canavalia brasiliensis) Explore P55915  Go to UniProtKB:  P55915

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.29	α = 90
b = 71.65	β = 90
c = 190.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-04-29 
Deposition Author(s): Sanz-Aparicio, J., Hermoso, J., Grangeiro, T.B., Calvete, J.J., Cavada, B.S.

Revision History  

• Version 1.0: 1998-04-29
  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: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection