1V6L

Peanut lectin-lactose complex in the presence of 9mer peptide (PVIWSSATG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report



Literature

Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure.

Kundhavai Natchiar, S.Arockia Jeyaprakash, A.Ramya, T.N.Thomas, C.J.Suguna, K.Surolia, A.Vijayan, M.

(2004) Acta Crystallogr D Biol Crystallogr 60: 211-219

  • DOI: 10.1107/S090744490302849X
  • Primary Citation of Related Structures:  
    1V6O, 1V6N, 1V6M, 1V6L, 1V6K, 1V6J, 1V6I

  • PubMed Abstract: 
  • Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in ...

    Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of these peptides as well as lactose. Low-pH crystal forms of the lectin-lactose complex similar to those obtained at neutral pH have also been grown. Thus, crystals of peanut lectin grown under different environmental conditions, at two pH values with and without sugar bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison between different structures shows that the lectin molecule is sturdy and that the effect of changes in pH, ligand binding and environment on it is small. The region involving the curved front beta-sheet and the loops around the second hydrophobic core is comparatively rigid. The back beta-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible, as is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing unusual structural features. Small consistent movements occur in the combining site upon sugar binding, although the site is essentially preformed.


    Related Citations: 
    • Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex
      Banerjee, R., Das, K., Ravishankar, R., Suguna, K., Surolia, A., Vijayan, M.
      (1996) J Mol Biol 259: 281
    • Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site
      Ravishankar, R., Thomas, C.J., Suguna, K., Surolia, A., Vijayan, M.
      (2001) Proteins 43: 260

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galactose-binding lectinABCD232Arachis hypogaeaMutation(s): 0 
Find proteins for P02872 (Arachis hypogaea)
Explore P02872 
Go to UniProtKB:  P02872
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
E, H
2 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
F, G
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900008
Query on PRD_900008
E, Halpha-lactoseOligosaccharide /  Nutrient

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Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004
F, Gbeta-lactoseOligosaccharide /  Nutrient

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.278α = 90
b = 124.636β = 90
c = 75.752γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: Atomic model, Data collection, Derived calculations, Structure summary