Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 26.69 kDa 
• Atom Count: 2181 
• Modelled Residue Count: 239 
• Deposited Residue Count: 239 
• Unique protein chains: 1

1GZC

High-Resolution crystal structure of Erythrina cristagalli lectin in complex with lactose

• DOI: 10.2210/pdb1GZC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Erythrina crista-galli
• Mutation(s): No 


• Deposited: 2002-05-17 Released: 2002-06-21 
• Deposition Author(s): Svensson, C., Krengel, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.226 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

High-Resolution Crystal Structures of Erythrina Cristagalli Lectin in Complex with Lactose and 2'-Alpha-L-Fucosyllactose and Correlation with Thermodynamic Binding Data

Svensson, C., Teneberg, S., Nilsson, C., Kjellberg, A., Schwarz, F., Sharon, N., Krengel, U.

(2002) J Mol Biol 321: 69

• PubMed: 12139934 
• DOI: 10.1016/s0022-2836(02)00554-5
• Primary Citation of Related Structures:  
  1GZ9, 1GZC


• PubMed Abstract: 
  

The primary sequence of Erythrina cristagalli lectin (ECL) was mapped by mass spectrometry, and the crystal structures of the lectin in complex with lactose and 2'-alpha-L-fucosyllactose were determined at 1.6A and 1.7A resolution, respectively. The two complexes were compared with the crystal structure of the closely related Erythrina corallodendron lectin (ECorL) in complex with lactose, with the crystal structure of the Ulex europaeus lectin II in complex with 2'-alpha-L-fucosyllactose, and with two modeled complexes of ECorL with 2'-alpha-L-fucosyl-N-acetyllactosamine. The molecular models are very similar to the crystal structure of ECL in complex with 2'-alpha-L-fucosyllactose with respect to the overall mode of binding, with the L-fucose fitting snugly into the cavity surrounded by Tyr106, Tyr108, Trp135 and Pro134 adjoining the primary combining site of the lectin. Marked differences were however noted between the models and the experimental structure in the network of hydrogen bonds and hydrophobic interactions holding the L-fucose in the combining site of the lectin, pointing to limitations of the modeling approach. In addition to the structural characterization of the ECL complexes, an effort was undertaken to correlate the structural data with thermodynamic data obtained from microcalorimetry, revealing the importance of the water network in the lectin combining site for carbohydrate binding.

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Organizational Affiliation: 

Department of Molecular Biotechnology and Center for Structural Biology, Chalmers University of Technology, P. O. Box 462, SE-405-30 Goteborg, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERYTHRINA CRISTA-GALLI LECTIN	A	239	Erythrina crista-galli	Mutation(s): 0
Find proteins for P83410 (Erythrina crista-galli) Explore P83410  Go to UniProtKB:  P83410

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LAT	Kd :  320000   nM  PDBBind
LAT	Kd:  320000   nM  Binding MOAD

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	B	beta-lactose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.226 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.8	α = 90
b = 81.8	β = 90
c = 126.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-17 
• Released Date: 2002-06-21 
Deposition Author(s): Svensson, C., Krengel, U.

Revision History  

• Version 1.0: 2002-06-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary