2BN0

Banana Lectin bound to Laminaribiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
RIPENING-ASSOCIATED PROTEINA, B141Musa 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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseC, D, E, F 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G36535HU
GlyCosmos:  G36535HU
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900024
Query on PRD_900024
C, D, E, Fbeta-laminaribioseOligosaccharide / Antimicrobial Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.8α = 90
b = 81.8β = 90
c = 147.2γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report




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: Atomic model, Data collection, Derived calculations, Structure summary