5O47

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

PDB DOI: https://doi.org/10.2210/pdb5O47/pdb

Classification: HYDROLASE
Organism(s): Phaffia rhodozyma
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2017-05-26 Released: 2018-11-28
Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.182
R-Value Work: 0.168
R-Value Observed: 0.169

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

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

(2018) ChemCatChem

DOI: https://doi.org/10.1002/cctc.201801171

Macromolecule Content

Total Structure Weight: 159.36 kDa
Atom Count: 12,016
Modelled Residue Count: 1,248
Deposited Residue Count: 1,330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-fructofuranosidase	A, B	665	Phaffia rhodozyma	Mutation(s): 1 Gene Names: INV
UniProt
Find proteins for J7HDY4 (Phaffia rhodozyma) Explore J7HDY4 Go to UniProtKB: J7HDY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J7HDY4
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	C, F	6		N-Glycosylation	Interactions Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	10		N-Glycosylation	Interactions Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H	2		N-Glycosylation	Interactions Focus chain E Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9WZ Query on 9WZ Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain YA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B]	Y [auth A], YA [auth B]	2-hydroxy-4-(2-hydroxyethyl)phenyl beta-D-fructofuranoside C₁₄ H₂₀ O₈ CNXXGYXVIZNKJW-YIYPIFLZSA-N		Interactions Focus chain Y [auth A] Focus chain YA [auth B]
9OK Query on 9OK Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B]	X [auth A], XA [auth B]	2-(3,4-dihydroxyphenyl)ethyl beta-D-fructofuranoside C₁₄ H₂₀ O₈ LKYHMBCDFKCNAO-YIYPIFLZSA-N		Interactions Focus chain X [auth A] Focus chain XA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] LA [auth B] I [auth A], J [auth A], K [auth A], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B]
975 Query on 975 Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	Z [auth A], ZA [auth B]	4-(2-hydroxyethyl)benzene-1,2-diol C₈ H₁₀ O₃ JUUBCHWRXWPFFH-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Focus chain ZA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain KA [auth A] SDF format, chain KB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A], KB [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.182
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.616	α = 90
b = 205.356	β = 90
c = 146.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-11-28

Deposition Author(s):

Ramirez-Escudero, M.

Sanz-Aparicio, J.

Revision History (Full details and data files)

Version 1.0: 2018-11-28
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: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary