1EHD

CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose.

Harata, K.Muraki, M.

(2000) J Mol Biol 297: 673-681

  • DOI: 10.1006/jmbi.2000.3594
  • Primary Citation of Related Structures:  
    1EHH, 1EHD

  • PubMed Abstract: 
  • Urtica dioica agglutinin is a small plant lectin that binds chitin. We purified the isolectin VI (UDA-VI) and crystal structures of the isolectin and its complex with tri-N-acetylchitotriose (NAG3) were determined by X-ray analysis. The UDA-VI consists of two domains analogous to hevein and the backbone folding of each domain is maintained by four disulfide bridges ...

    Urtica dioica agglutinin is a small plant lectin that binds chitin. We purified the isolectin VI (UDA-VI) and crystal structures of the isolectin and its complex with tri-N-acetylchitotriose (NAG3) were determined by X-ray analysis. The UDA-VI consists of two domains analogous to hevein and the backbone folding of each domain is maintained by four disulfide bridges. The sequence similarity of the two domains is not high (42 %) but their backbone structures are well superimposed except some loop regions. The chitin binding sites are located on the molecular surface at both ends of the dumbbell-shape molecule. The crystal of the NAG3 complex contains two independent molecules forming a protein-sugar 2:2 complex. One NAG3 molecule is sandwiched between two independent UDA-VI molecules and the other sugar molecule is also sandwiched by one UDA-VI molecule and symmetry-related another one. The sugar binding site of N-terminal domain consists of three subsites accommodating NAG3 while two NAG residues are bound to the C-terminal domain. In each sugar-binding site, three aromatic amino acid residues and one serine residue participate to the NAG3 binding. The sugar rings bound to two subsites are stacked to the side-chain groups of tryptophan or histidine and a tyrosine residue is in face-to-face contact with an acetylamino group, to which the hydroxyl group of a serine residue is hydrogen-bonded. The third subsite of the N-terminal domain binds a NAG moiety with hydrogen bonds. The results suggest that the triad of aromatic amino acid residues is intrinsic in sugar binding of hevein-like domains.


    Organizational Affiliation

    Biomolecules Department, National Institute of Bioscience and Human Technology, 1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan. harata@nibh.go.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AGGLUTININ ISOLECTIN VIA89Urtica dioicaMutation(s): 0 
Gene Names: chia5.5.2chia5.5.1
UniProt
Find proteins for Q9S7B3 (Urtica dioica)
Explore Q9S7B3 
Go to UniProtKB:  Q9S7B3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.92α = 90
b = 41.29β = 90
c = 76.45γ = 90
Software Package:
Software NamePurpose
MADNESSdata collection
MERGEFdata reduction
MIRPHSmodel building
X-PLORrefinement
MADNESSdata reduction
MERGEFdata scaling
MIRPHSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2000-02-20 
  • Released Date: 2000-04-05 
  • Deposition Author(s): Harata, K., Muraki, M.

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-05
    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 1.4: 2018-04-18
    Changes: Data collection
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence