1JPC

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 2.0 of the entry. See complete history. 


Literature

The 2.0 A structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes.

Wright, C.S., Hester, G.

(1996) Structure 4: 1339-1352

  • DOI: https://doi.org/10.1016/s0969-2126(96)00141-4
  • Primary Citation of Related Structures:  
    1JPC

  • PubMed Abstract: 

    Galanthus nivalis agglutinin (GNA), a mannose-specific lectin from snowdrop bulbs, is a tetrameric member of the family of Amaryllidaceae lectins that exhibit antiviral activity towards HIV. Its subunits are composed of three pseudo-symmetrically related beta sheet domains, each with a conserved mannose-binding site. Crystal structures of monosaccharide and disaccharide complexes of GNA have revealed that all 12 binding sites of the tetramer are functional, and that the degree of occupancy is dependent on the availability of subsidiary interactions from neighboring subunits. The complex of GNA with a branched mannopentaose ((Manalpha1,6-(alpha1, 3-Man)Man-alpha1,6-(alpha1,3-Man)Man) described here simulates a more biologically relevant complex.

    • Organizational Affiliation: 

    Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia 23298, USA. cswright@gems.vcu.edu


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AGGLUTININ109Galanthus nivalisMutation(s): 0 
UniProt
Find proteins for P30617 (Galanthus nivalis)
Explore P30617 
Go to UniProtKB:  P30617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30617
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
B, D
3N/A
Glycosylation Resources
GlyTouCan:  G00619DD
GlyCosmos:  G00619DD
GlyGen:  G00619DD
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G77384RA
GlyCosmos:  G77384RA
GlyGen:  G77384RA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.339α = 90
b = 96.339β = 90
c = 68.635γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-02-05
    Changes: Advisory, Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary