5O47

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructosyl-hydroxytyrosol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fructosylation of Hydroxytyrosol by the beta-Fructofuranosidase from Xanthophyllomyces dendrorhous: Insights into the Molecular Basis of the Enzyme Specificity

Ramirez-Escudero, M.Poveda, a.Ballesteros, A.O.Plou, F.J.

(2018) Chem.Cat.Chem --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-fructofuranosidase
A, B
665Phaffia rhodozymaMutation(s): 1 
Gene Names: INV
Find proteins for J7HDY4 (Phaffia rhodozyma)
Go to UniProtKB:  J7HDY4
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9WZ
Query on 9WZ

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A, B
(2~{S},3~{S},4~{S},5~{R})-2-[4-(2-hydroxyethyl)-2-oxidanyl-phenoxy]-2,5-bis(hydroxymethyl)oxolane-3,4-diol
C14 H20 O8
CNXXGYXVIZNKJW-YIYPIFLZSA-N
 Ligand Interaction
975
Query on 975

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A, B
4-(2-hydroxyethyl)benzene-1,2-diol
C8 H10 O3
JUUBCHWRXWPFFH-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
9OK
Query on 9OK

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Download CCD File 
A, B
fructosyl-hydroxytyrosol
C14 H20 O8
LKYHMBCDFKCNAO-YIYPIFLZSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.616α = 90.00
b = 205.356β = 90.00
c = 146.940γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-28
    Type: Initial release