4TYS | pdb_00004tys

Crystal structure of Canavalia maritima lectin (ConM) complexed with a dinucleotide

• PDB DOI: https://doi.org/10.2210/pdb4TYS/pdb

• Classification: Carbohydrate binding protein
• Organism(s): Canavalia lineata
• Mutation(s): No 


• Deposited: 2014-07-09 Released: 2015-07-22 
• Deposition Author(s): Vieira, D.B.H.A., Delatorre, P., Silva-Filho, J.C., Nobrega, R.B., Cavada, B.S., Rocha, B.A.M., Lima, E.M., Teixeira, C.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of Canavalia maritima lectin (ConM) complexed with a dinucleotide

Vieira, D.B.H.A., Delatorre, P., Cavada, B.S., Silva-Filho, J.C., Nobrega, R.B., Teixeira, C.S., Lima, E.M., 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 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 153.53 kDa 
• Atom Count: 10,750 
• Modelled Residue Count: 1,393 
• Deposited Residue Count: 1,422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B, C, D, E, F	237	Canavalia lineata	Mutation(s): 0
UniProt
Find proteins for P81460 (Canavalia lineata) Explore P81460  Go to UniProtKB:  P81460

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3XZ	G [auth E]	bis{[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methyl} hydrogen phosphate C20 H25 N10 O8 P PPQXTUORNPDZDR-PRSXHHODSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.69	α = 90
b = 140.57	β = 90
c = 199.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Vieira, D.B.H.A., Delatorre, P., Silva-Filho, J.C., Nobrega, R.B., Cavada, B.S., Rocha, B.A.M., Lima, E.M., Teixeira, C.S.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Data collection
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations