2FMD | pdb_00002fmd

Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 

Literature

Structural basis of carbohydrate recognition by a Man(alpha1-2)Man-specific lectin from Bowringia milbraedii.

Buts, L., Garcia-Pino, A., Wyns, L., Loris, R.

(2006) Glycobiology 16: 635-640

  • DOI: https://doi.org/10.1093/glycob/cwj109
  • Primary Citation Related Structures: 
    2FMD

  • PubMed Abstract: 

    The crystal structure of the seed lectin from the tropical legume Bowringia milbraedii was determined in complex with the disaccharide ligand Man(alpha1-2)Man. In solution, the protein exhibits a dynamic dimer-tetramer equilibrium, consistent with the concanavalin A-type tetramer observed in the crystal. Contacts between the tetramers are mediated almost exclusively through the carbohydrate ligand, resulting in a crystal lattice virtually identical to that of the concanavalin-A:Man(alpha1-2)Man complex, even though both proteins have less than 50% sequence identity. The disaccharide binds exclusively in a "downstream" binding mode, with the non-reducing mannose occupying the monosaccharide-binding site. The reducing mannose is bound in a predominantly polar subsite involving Tyr131, Gln218, and Tyr219.

    • Organizational Affiliation: 
    • Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel and Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussels, Belgium. lievbuts@vub.ac.be

Macromolecule Content 

  • Total Structure Weight: 26.02 kDa 
  • Atom Count: 1,974 
  • Modeled Residue Count: 232 
  • Deposited Residue Count: 240 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lectin240Leucomphalos mildbraediiMutation(s): 0 
UniProt
Find proteins for P42088 (Leucomphalos mildbraedii)
Explore P42088 
Go to UniProtKB:  P42088
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42088
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G53402KW
GlyCosmos: G53402KW
GlyGen: G53402KW

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.603α = 90
b = 86.351β = 90
c = 91.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary