1CR7

PEANUT LECTIN-LACTOSE COMPLEX MONOCLINIC FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 260-270

  • Primary Citation of Related Structures:  1CQ9
  • Also Cited By: 1V6I, 1V6J, 1V6K, 1V6L, 1V6M, 1V6N, 1V6O

  • PubMed Abstract: 
  • The crystal structures of a monoclinic and a triclinic form of the peanut lectin-lactose complex, grown at pH 4.6, have been determined. They contain two and one crystallographically independent tetramers, respectively. The unusual "open" quaternary ...

    The crystal structures of a monoclinic and a triclinic form of the peanut lectin-lactose complex, grown at pH 4.6, have been determined. They contain two and one crystallographically independent tetramers, respectively. The unusual "open" quaternary structure of the lectin, observed in the orthorhombic complex grown in neutral pH, is retained at the acidic pH. The sugar molecule is bound to three of the eight subunits in the monoclinic crystals, whereas the combining sites in four are empty. The lectin-sugar interactions are almost the same at neutral and acidic pH. A comparison of the sugar-bound and free subunits indicates that the geometry of the combining site is relatively unaffected by ligand binding. The combining site of the eighth subunit in the monoclinic crystals is bound to a peptide stretch in a loop from a neighboring molecule. The same interaction exists in two subunits of the triclinic crystals, whereas density corresponding to sugar exists in the combining sites of the other two subunits. Solution studies show that oligopeptides with sequences corresponding to that in the loop bind to the lectin at acidic pH, but only with reduced affinity at neutral pH. The reverse is the case with the binding of lactose to the lectin. A comparison of the neutral and acidic pH crystal structures indicates that the molecular packing in the latter is directed to a substantial extent by the increased affinity of the peptide loop to the combining site at acidic pH.


    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.USA 91: 227
    • 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
    • The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges
      Ravishankar, R.,Ravindran, M.,Suguna, K.,Surolia, A.,Vijayan, M.
      (1997) Curr.Sci. 72: 855
    • Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N- Acetyllactosamine and a Comparative Study of Carbohydrate Binding in Gal/ Galnac-Specific Legume Lectins
      Ravishankar, R.,Suguna, K.,Surolia, A.,Vijayan, M.
      (1999) Acta Crystallogr.,Sect.D 55: 1375


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LECTIN
A, B, C, D, E, F, G, H
236Arachis hypogaeaN/A
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, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, E
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B, E
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 128.320α = 90.00
b = 126.820β = 116.14
c = 85.610γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-21
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description