PDBsum entry: 1axz

Lectin

PDB id: 1axz

Contents

Protein chain

239 a.a. *

Ligands

NAG-FUC-NAG-BMA-XYP-MAN-MAN

GLA-GAL

Metals

_CA

_MN

Waters ×135

* Residue conservation analysis

PDB id:

1axz

Name:

Lectin

Title:

Erythrina corallodendron lectin in complex with d-galactose

Structure:

Lectin. Chain: a

Source:

Erythrina corallodendron. Organism_taxid: 3843

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

1.95Å R-factor: 0.179 R-free: 0.206

Authors:

B.Shaanan,S.Elgavish

Key ref:

S.Elgavish and B.Shaanan (1998). Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides. J Mol Biol, 277, 917-932. PubMed id: 9545381 DOI: 10.1006/jmbi.1998.1664

Date:

24-Oct-97 Release date: 06-May-98

Protein chain

P16404  (LEC_ERYCO) -  Lectin

Seq: 281 a.a.

Struc: 239 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (2 terms)

DOI no: 10.1006/jmbi.1998.1664

J Mol Biol 277:917-932 (1998)

PubMed id: 9545381

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

S.Elgavish, B.Shaanan.

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.

Selected figure(s)

Figure 1.
Figure 1. The dimer interface in EcorL (stereo). The two EcorL monomers forming the dimer are related by the crystallographic 2-fold axis at 0,y,1/2, which is slightly tilted and roughly in the plane of the Figure. Residues emanating from β-strands of each monomer interdigitate and form direct or water-mediated hydrogen bonds, as well as van der Waals contacts (see also Table 2 and Figure 2). Monomer A, strands in green, side-chains and water molecules, depicted as spheres, in cyan; monomer B, strands in red, side-chains and water molecules in yellow; residues are labelled in the colour of the corresponding monomer. Water molecule 606 on the 2-fold axis is depicted as a large orange sphere.

Figure 3.
Figure 3. Schematic, two-dimensional diagrams (LIGPLOT; [Wallace et al 1995]) of the combining sites of EcorL and its complexes. Carbon atoms are depicted in black, oxygen in red, nitrogen in blue, hydrogen bonds (broken lines) and their length in green. The water molecules are depicted as spheres in colours corresponding to the colour scheme in Figure 4. a, ECPRO; b, ECGAL (only the β-anomer of Gal is depicted); c, ECGNAL; d, ECLAC; e, ECNAL.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 917-932) copyright 1998.

Figures were selected by an automated process.