5EO7 | pdb_00005eo7

Crystal structure of AOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.241 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

Makyio, H.Shimabukuro, J.Suzuki, T.Imamura, A.Ishida, H.Kiso, M.Ando, H.Kato, R.

(2016) Biochem Biophys Res Commun 477: 477-482

  • DOI: https://doi.org/10.1016/j.bbrc.2016.06.069
  • Primary Citation of Related Structures:  
    5EO7, 5EO8

  • PubMed Abstract: 

    The crystal structure of AOL (a fucose-specific lectin of Aspergillus oryzae) has been solved by SAD (single-wavelength anomalous diffraction) and MAD (multi-wavelength anomalous diffraction) phasing of seleno-fucosides. The overall structure is a six-bladed β-propeller similar to that of other fucose-specific lectins. The fucose moieties of the seleno-fucosides are located in six fucose-binding sites. Although the Arg and Glu/Gln residues bound to the fucose moiety are common to all fucose-binding sites, the amino-acid residues involved in fucose binding at each site are not identical. The varying peak heights of the seleniums in the electron density map suggest that each fucose-binding site has a different carbohydrate binding affinity.


  • Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted protein
A, B, C
310Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090001000189
UniProt
Find proteins for Q2UNX8 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2UNX8 
Go to UniProtKB:  Q2UNX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2UNX8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFU
Query on SFU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
methyl 1-seleno-alpha-L-fucopyranoside
C7 H14 O4 Se
VHTNTJQSKJZERS-XUVCUMPTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
V [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.241 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.161α = 90
b = 196.852β = 90
c = 110.605γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SFUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary