6VB8 | pdb_00006vb8

Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid

• PDB DOI: https://doi.org/10.2210/pdb6VB8/pdb

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


• Deposited: 2019-12-18 Released: 2020-12-23 
• Deposition Author(s): Bezerra, E.H.S., Queiroz, P.P., da Silva, F.M.S., Girao, M.S., Sales, M.V., Paiva, C.P.S., Freire, V.N., Rocha, B.A.M.
• Funding Organization(s): Coordination for the Improvement of Higher Education Personnel

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural insights into phytohormone interaction to plant lectin ConBr

Bezerra, E.H.S., Sales, M.V., Girao, M.S., da Silva, F.M.S., Queiroz, P.P., Paiva, C.P.S., Freire, V.N., Rocha, B.A.M.

To be published.

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)

Biological Assembly Evidence: native gel electrophoresis, gel filtration

Macromolecule Content 

• Total Structure Weight: 26.13 kDa 
• Atom Count: 1,855 
• Modeled Residue Count: 233 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-Br	A	237	Canavalia brasiliensis	Mutation(s): 0
UniProt
Find proteins for P55915 (Canavalia brasiliensis) Explore P55915  Go to UniProtKB:  P55915

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IAC (Subject of Investigation/LOI)	H [auth A]	1H-INDOL-3-YLACETIC ACID C10 H9 N O2 SEOVTRFCIGRIMH-UHFFFAOYSA-N
DBB	G [auth A]	D-ALPHA-AMINOBUTYRIC ACID C4 H9 N O2 QWCKQJZIFLGMSD-GSVOUGTGSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.806	α = 90
b = 72.427	β = 90
c = 99.272	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling
XDS	data reduction
MxCuBE	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Bezerra, E.H.S., Queiroz, P.P., da Silva, F.M.S., Girao, M.S., Sales, M.V., Paiva, C.P.S., Freire, V.N., Rocha, B.A.M.

---

Funding Organization	Location	Grant Number
Coordination for the Improvement of Higher Education Personnel	Brazil	--

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection