PDBsum entry 1iqb

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protein metals Protein-protein interface(s) links
Sugar binding protein PDB id
Protein chains
89 a.a. *
_ZN ×2
Waters ×87
* Residue conservation analysis
PDB id:
Name: Sugar binding protein
Title: Crystal structure of urtica dioica agglutinin isolectin i
Structure: Agglutinin isolectin i. Chain: a, b. Fragment: residues 1-89. Mutation: yes
Source: Urtica dioica. Great nettle. Organism_taxid: 3501
1.90Å     R-factor:   0.205     R-free:   0.260
Authors: K.Harata,W.D.Schubert,M.Muraki
Key ref:
K.Harata et al. (2001). Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site. Acta Crystallogr D Biol Crystallogr, 57, 1513-1517. PubMed id: 11679714 DOI: 10.1107/S090744490101232X
15-Jul-01     Release date:   07-Nov-01    
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Protein chains
Pfam   ArchSchema ?
P11218  (AGI_URTDI) -  Lectin/endochitinase 1
372 a.a.
89 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Chitinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chitin binding     1 term  


DOI no: 10.1107/S090744490101232X Acta Crystallogr D Biol Crystallogr 57:1513-1517 (2001)
PubMed id: 11679714  
Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.
K.Harata, W.D.Schubert, M.Muraki.
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.
  Selected figure(s)  
Figure 2.
Figure 2 A superposition of the N-terminal domain (red) and the C-terminal domain (red), respectively, for the two independent molecules. Side-chain groups of amino-acid residues involving in the sugar binding are rendered in magenta (domain 1) and cyan (domain 2).
Figure 3.
Figure 3 A superposition of the independent molecules of UDA-I (molecule 1 in red, molecule 2 in yellow) and the structure of UDA-VI (green). Amino-acid side chains involved in sugar binding are shown. Amino-acid residues differing between UDA-I and UDA-VI are depicted for molecule 1 and are labelled in red.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1513-1517) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544965 Y.Kezuka, M.Kojima, R.Mizuno, K.Suzuki, T.Watanabe, and T.Nonaka (2010).
Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
  Proteins, 78, 2295-2305.
PDB code: 3iwr
17324258 C.Lans, N.Turner, T.Khan, G.Brauer, and W.Boepple (2007).
Ethnoveterinary medicines used for ruminants in British Columbia, Canada.
  J Ethnobiol Ethnomed, 3, 11.  
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