2BMZ

Banana Lectin bound to Xyl-b1,3 Man-a-O-Methyl (XM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of Banana Lectin Reveals a Novel Second Sugar Binding Site.

Meagher, J.L.Winter, H.C.Ezell, P.Goldstein, I.J.Stuckey, J.A.

(2005) Glycobiology 15: 1033

  • DOI: https://doi.org/10.1093/glycob/cwi088
  • Primary Citation of Related Structures:  
    2BMY, 2BMZ, 2BN0

  • PubMed Abstract: 

    Banana lectin (Banlec) is a dimeric plant lectin from the jacalin-related lectin family. Banlec belongs to a subgroup of this family that binds to glucose/mannose, but is unique in recognizing internal alpha1,3 linkages as well as beta1,3 linkages at the reducing termini. Here we present the crystal structures of Banlec alone and with laminaribiose (LAM) (Glcbeta1, 3Glc) and Xyl-beta1,3-Man-alpha-O-Methyl. The structure of Banlec has a beta-prism-I fold, similar to other family members, but differs from them in its mode of sugar binding. The reducing unit of the sugar is inserted into the binding site causing the second saccharide unit to be placed in the opposite orientation compared with the other ligand-bound structures of family members. More importantly, our structures reveal the presence of a second sugar binding site that has not been previously reported in the literature. The residues involved in the second site are common to other lectins in this family, potentially signaling a new group of mannose-specific jacalin-related lectins (mJRL) with two sugar binding sites.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIPENING-ASSOCIATED PROTEIN
A, B
141Musa acuminataMutation(s): 0 
UniProt
Find proteins for O22321 (Musa acuminata)
Explore O22321 
Go to UniProtKB:  O22321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22321
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-3)-methyl alpha-D-mannopyranoside
C, D, E, F
2N/A
Glycosylation Resources
GlyTouCan:  G12515RY
GlyCosmos:  G12515RY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.623α = 90
b = 81.623β = 90
c = 146.815γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-16
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary