Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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This is version 2.1 of the entry. See complete history


Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides.

Elgavish, S.Shaanan, B.

(1998) J Mol Biol 277: 917-932

  • DOI: https://doi.org/10.1006/jmbi.1998.1664
  • Primary Citation of Related Structures:  
    1AX0, 1AX1, 1AX2, 1AXY, 1AXZ

  • PubMed Abstract: 

    The structures of the Erythrina corallodendron lectin (EcorL) and of its complexes with galactose, N-acetylgalactosamine, lactose and N-acetyllactosamine were determined at a resolution of 1.9 to 1.95 A. The final R-values of the five models are in the range 0.169 to 0.181. The unusual, non-canonical, dimer interface of EcorL is made of beta-strands from the two monomers, which face one another in a "hand-shake" mode. The galactose molecule in the primary binding site is bound in an identical way in all four complexes. Features of the electrostatic potential of the galactose molecule match those of the potential in the combining site, thus probably pointing to the contribution of the electrostatic energy to determining the orientation of the ligand. No conformational change occurs in the protein upon binding the ligand. Subtle variations in the binding mode of the second monosaccharide (glucose in the complex with lactose and N-acetylglucosamine in the complex with N-acetyllactosamine) were observed. The mobility of Gln219 is lower in the complexes with the disaccharides than in the complexes with the monosaccharides, indicating further recruitment of this residue to ligand binding through more extensive hydrogen bonding in the former complexes. Water molecules that have been located in the combining sites of the five structures undergo rearrangement in response to binding of the different ligands. The new structural information is in qualitative agreement with thermodynamic data on the binding to EcorL.

  • Organizational Affiliation

    The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LECTIN239Erythrina corallodendronMutation(s): 0 
Find proteins for P16404 (Erythrina corallodendron)
Explore P16404 
Go to UniProtKB:  P16404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16404
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G26295XE
GlyCosmos:  G26295XE
GlyGen:  G26295XE
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NGA PDBBind:  1AX0 Kd: 7.46e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.22α = 90
b = 72.98β = 113.33
c = 71.26γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-06
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-04-03
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary