2DVD

Crystal structure of peanut lectin GAL-ALPHA-1,3-GAL complex

• PDB DOI: https://doi.org/10.2210/pdb2DVD/pdb

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


• Deposited: 2006-07-31 Released: 2006-11-07 
• Deposition Author(s): Natchiar, S.K., Srinivas, O., Mitra, N., Surolia, A., Jayaraman, N., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.232 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (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: 102.97 kDa 
• Atom Count: 8,135 
• 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-beta-D-galactopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G95894VW GlyCosmos:  G95894VW GlyGen:  G95894VW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth A], N [auth B], Q [auth C], T [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	J [auth A], M [auth B], P [auth C], S [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth A], L [auth B], O [auth C], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.232 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.44	α = 90
b = 124.64	β = 90
c = 75.69	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Natchiar, S.K., Srinivas, O., Mitra, N., Surolia, A., Jayaraman, N., Vijayan, M.

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary