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 1.3 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
  • Also Cited By: 2DVG, 2DVF, 2DVD, 2DVB, 2DVA, 2DV9, 2DH1, 1V6L, 1V6K, 1V6J, 1V6I

  • 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 lec ...

    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: 
    • 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
    • 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.USA 91: 227


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEANUT LECTIN
A, B, C, D
236Arachis hypogaeaMutation(s): 0 
Find proteins for P02872 (Arachis hypogaea)
Go to UniProtKB:  P02872
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LBT
Query on LBT

Download SDF File 
Download CCD File 
A, B, D
ALPHA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-XLOQQCSPSA-N
 Ligand Interaction
LAT
Query on LAT

Download SDF File 
Download CCD File 
C
BETA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-DCSYEGIMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKi: 1370000 nM BINDINGMOAD
LBTKi: 1370000 nM BINDINGMOAD
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 = 129.300α = 90.00
b = 126.900β = 90.00
c = 76.900γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other