2DH1

Crystal structure of peanut lectin lactose-azobenzene-4,4'-dicarboxylic acid-lactose complex

• PDB DOI: https://doi.org/10.2210/pdb2DH1/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Arachis hypogaea
• Mutation(s): No 


• Deposited: 2006-03-17 Released: 2006-08-15 
• Deposition Author(s): Natchiar, S.K., Srinivas, O., Nivedita, M., Sagarika, D., Jayaraman, N., Surolia, A., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.65 Å
• R-Value Free: 
  0.377 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.355 (Depositor), 0.370 (DCC) 
• R-Value Observed: 
  0.356 (Depositor) 

Starting Model: experimental

Literature

Multivalency in lectins - A crystallographic, modelling and light-scattering study involving peanut lectin and a bivalent ligand

Natchiar, S.K., Srinivas, O., Nivedita, M., Sagarika, D., Jayaraman, N., Surolia, A., Vijayan, M.

(2006) Curr Sci 90: 1230-1237

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.84 kDa 
• Atom Count: 928 
• Modelled Residue Count: 928 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding lectin	A, B, C, D	236	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for P02872 (Arachis hypogaea) Explore P02872  Go to UniProtKB:  P02872

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.65 Å
• R-Value Free:  0.377 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.355 (Depositor), 0.370 (DCC) 
• R-Value Observed: 0.356 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.75	α = 90
b = 92.75	β = 90
c = 473.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Natchiar, S.K., Srinivas, O., Nivedita, M., Sagarika, D., Jayaraman, N., Surolia, A., Vijayan, M.

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description