5NSL

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and hydroxytyrosol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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

Miquez, N.Ramirez-Escudero, M.Poveda, A.Ballesteros, O.Sanz-Aparicio, J.Plou, F.J.

(2018) ChemCatChem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-fructofuranosidase
A, B
665Phaffia rhodozymaMutation(s): 1 
Gene Names: INV
UniProt
Find proteins for J7HDY4 (Phaffia rhodozyma)
Explore J7HDY4 
Go to UniProtKB:  J7HDY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7HDY4
Glycosylation
Glycosylation Sites: 14
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, G
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83161QT
GlyCosmos:  G83161QT
GlyGen:  G83161QT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G92805XC
GlyCosmos:  G92805XC
GlyGen:  G92805XC
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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AC [auth B]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
AC [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
QB [auth B],
R [auth A],
RB [auth B],
S [auth A],
SB [auth B],
T [auth A],
TB [auth B],
U [auth A],
UB [auth B],
V [auth A],
VB [auth B],
WB [auth B],
XB [auth B],
YB [auth B],
ZB [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FRU
Query on FRU

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BC [auth B],
W [auth A]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
975
Query on 975

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
CC [auth B]
DA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
CC [auth B],
DA [auth A],
DC [auth B],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
IA [auth A],
IC [auth B],
JA [auth A],
JC [auth B],
KA [auth A],
KC [auth B],
LA [auth A],
LC [auth B],
MA [auth A],
MC [auth B],
NA [auth A],
NC [auth B],
OA [auth A],
OC [auth B],
PA [auth A],
PC [auth B],
QA [auth A],
QC [auth B],
RA [auth A],
RC [auth B],
SA [auth A],
SC [auth B],
X [auth A],
Y [auth A],
Z [auth A]
4-(2-hydroxyethyl)benzene-1,2-diol
C8 H10 O3
JUUBCHWRXWPFFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth A]
AD [auth B]
BB [auth A]
BD [auth B]
CB [auth A]
AB [auth A],
AD [auth B],
BB [auth A],
BD [auth B],
CB [auth A],
CD [auth B],
DB [auth A],
DD [auth B],
EB [auth A],
ED [auth B],
FB [auth A],
FD [auth B],
GB [auth A],
GD [auth B],
HB [auth A],
HD [auth B],
IB [auth A],
ID [auth B],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
MB [auth A],
NB [auth A],
OB [auth A],
PB [auth A],
TA [auth A],
TC [auth B],
UA [auth A],
UC [auth B],
VA [auth A],
VC [auth B],
WA [auth A],
WC [auth B],
XA [auth A],
XC [auth B],
YA [auth A],
YC [auth B],
ZA [auth A],
ZC [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.86α = 90
b = 206.124β = 90
c = 145.529γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary