2PEL

PEANUT LECTIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

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: 281-296

  • DOI: 10.1006/jmbi.1996.0319
  • Primary Citation of Related Structures:  
    2PEL

  • PubMed Abstract: 
  • The structure of the complex of the tetrameric peanut lectin with lactose has been refined to an R-value of 16.4% using 2.25 angstroms resolution X-ray diffraction data. The subunit conformation in the structure is similar to that in other legume lectins except in the loops ...

    The structure of the complex of the tetrameric peanut lectin with lactose has been refined to an R-value of 16.4% using 2.25 angstroms resolution X-ray diffraction data. The subunit conformation in the structure is similar to that in other legume lectins except in the loops. It has been shown that in the tertiary structure of legume lectins, the short five-stranded sheet plays a major role in connecting the larger flat six-stranded and curved seven-stranded sheets. Furthermore, the loops that connect the strands at the two ends of the seven-stranded sheet curve toward and interact with each other to produce a second hydrophobic core in addition to the one between the two large sheets. The protein-lactose interactions involve the invariant features observed in other legume lectins in addition to those characteristic of peanut lectin. The "open" quaternary association in peanut lectin is stabilised by hydrophobic, hydrogen-bonded and water-mediated interactions. Contrary to the earlier belief, the structure of peanut lectin demonstrates that the variability in quaternary association in legume lectins, despite all of them having nearly the same tertiary structure, is not necessarily caused by covalently bound carbohydrate. An attempt has been made to provide a structural rationale for this variability, on the basis of buried surface areas during dimerisation. A total of 45 water molecules remain invariant when the hydration shells of the four subunits are compared. A majority of them appear to be involved in stabilising loops.


    Related Citations: 
    • Crystal Structure of Peanut Lectin, a Protein with an Unusual Quaternary Structure
      Banerjee, R., Mande, S.C., Ganesh, V., Das, K., Dhanaraj, V., Mahanta, S.K., Suguna, K., Surolia, A., Vijayan, M.
      (1994) Proc Natl Acad Sci U S A 91: 227
    • Preparation and Preliminary X-Ray Studies of Three Acidic Ph Crystal Forms of the Anti-T Lectin from Peanut (Arachis Hypogaea)
      Salunke, D.M., Khan, M.I., Surolia, A., Vijayan, M.
      (1983) FEBS Lett 156: 127
    • Crystallization and Preliminary X-Ray Studies of the Anti-T Lectin from Peanut (Arachis Hypogaea)
      Salunke, D.M., Khan, M.I., Surolia, A., Vijayan, M.
      (1982) J Mol Biol 154: 177

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEANUT LECTINA, B, C, D236Arachis 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-glucopyranoseE, F, H2 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseG2 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900008
Query on PRD_900008
E, F, Halpha-lactoseOligosaccharide /  Nutrient

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.3α = 90
b = 126.9β = 90
c = 76.9γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary