Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 51.62 kDa 
• Atom Count: 3820 
• Modelled Residue Count: 456 
• Deposited Residue Count: 466 
• Unique protein chains: 2

1LEN

REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS RESOLUTION

• PDB DOI: 10.2210/pdb1LEN/pdb

• Classification: LECTIN
• Organism(s): Lens culinaris
• Mutation(s): No 


• Deposited: 1993-11-17 Released: 1994-01-31 
• Deposition Author(s): Van Overberge, D., Loris, R., Wyns, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.175 

Literature

Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.

Loris, R., Van Overberge, D., Dao-Thi, M.H., Poortmans, F., Maene, N., Wyns, L.

(1994) Proteins 20: 330-346

• PubMed: 7731952 
• DOI: 10.1002/prot.340200406
• Primary Citation of Related Structures:  
  1LEN, 2LAL


• PubMed Abstract: 
  

The structures of two crystal forms of lentil lectin are determined and refined at high resolution. Orthorhombic lentil lectin is refined at 1.80 A resolution to an R-factor of 0.184 and monoclinic lentil lectin at 1.75 A resolution to an R-factor of 0.175. These two structures are compared to each other and to the other available legume lectin structures. The monosaccharide binding pocket of each lectin monomer contains a tightly bound phosphate ion. This phosphate makes hydrogen bonding contacts with Asp-81 beta, Gly-99 beta, and Asn-125 beta, three residues that are highly conserved in most of the known legume lectin sequences and essential for monosaccharide recognition in all legume lectin crystal structures described thus far. A detailed analysis of the composition and properties of the hydrophobic contact network and hydrophobic nuclei in lentil lectin is presented. Contact map calculations reveal that dense clusters of nonpolar as well as polar side chains play a major role in secondary structure packing. This is illustrated by a large cluster of 24 mainly hydrophobic amino acids that is responsible for the majority of packing interactions between the two beta-sheets. Another series of four smaller and less hydrophobic clusters is found to mediate the packing of a number of loop structures upon the front sheet. A very dense, but not very conserved cluster is found to stabilize the transition metal binding site. The highly conserved and invariant nonpolar residues are distributed asymmetrically over the protein.

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Related Citations: 

• Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin
  Loris, R., Steyaert, J., Maes, D., Lisgarten, J., Pickersgill, R., Wyns, L.
  (1993) Biochemistry 32: 8772

• Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
  Loris, R., Lisgarten, J., Maes, D., Pickersgill, R., Korber, F., Reynolds, C., Wyns, L.
  (1992) J Mol Biol 223: 579

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Organizational Affiliation: 

Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Sint-Genesius-Rode, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LECTIN	A, C	181	Lens culinaris	Mutation(s): 0
UniProt
Find proteins for P02870 (Lens culinaris) Explore P02870  Go to UniProtKB:  P02870

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LECTIN	B, D	52	Lens culinaris	Mutation(s): 0
UniProt
Find proteins for P02870 (Lens culinaris) Explore P02870  Go to UniProtKB:  P02870

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	F [auth A], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	G [auth A], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.49	α = 90
b = 56.37	β = 104.4
c = 82.73	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-11-17 
• Released Date: 1994-01-31 
Deposition Author(s): Van Overberge, D., Loris, R., Wyns, L.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2020-09-09
  Changes: Database references, Derived calculations