1IQB

Crystal Structure of Urtica dioica Agglutinin Isolectin I

• PDB DOI: https://doi.org/10.2210/pdb1IQB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Urtica dioica
• Mutation(s): No 


• Deposited: 2001-07-15 Released: 2001-11-07 
• Deposition Author(s): Harata, K., Schubert, W.D., Muraki, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.260 
• R-Value Work: 0.205 

Literature

Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.

Harata, K., Schubert, W.D., Muraki, M.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1513-1517

• PubMed: 11679714 
• DOI: https://doi.org/10.1107/s090744490101232x
• Primary Citation of Related Structures:  
  1IQB


• PubMed Abstract: 
  

  Ultica dioica agglutinin, a plant lectin from the stinging nettle, consists of a total of seven individual isolectins. One of these structures, isolectin I, was determined at 1.9 A resolution by the X-ray method. The crystals belong to the space group P2(1) and the asymmetric unit contains two molecules related by local twofold symmetry. The molecule consists of two hevein-like chitin-binding domains lacking distinct secondary structure, but four disulfide bonds in each domain maintain the tertiary structure. The backbone structure of the two independent molecules is essentially identical and this is similarly true of the sugar-binding sites. In the crystal, the C-terminal domains bind Zn(2+) ions at the sugar-binding site. Owing to their location near a pseudo-twofold axis, the two zinc ions link the two independent molecules in a tail-to-tail arrangement: thus, His47 of molecule 1 and His67 of molecule 2 coordinate the first zinc ion, while the second zinc ion links Asp75 of molecule 1 and His47 of molecule 2.

---

Organizational Affiliation: 

Biological Information Research Center, AIST, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18.95 kDa 
• Atom Count: 1,381 
• Modelled Residue Count: 178 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ ISOLECTIN I	A, B	89	Urtica dioica	Mutation(s): 0
UniProt
Find proteins for P11218 (Urtica dioica) Explore P11218  Go to UniProtKB:  P11218

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.260 
• R-Value Work: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.71	α = 90
b = 42.11	β = 101.55
c = 62.59	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
MERGF	data reduction
X-PLOR	model building
X-PLOR	refinement
MADNESS	data reduction
MERGEF	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-07 
Deposition Author(s): Harata, K., Schubert, W.D., Muraki, M.

Revision History  

• Version 1.0: 2001-11-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description