5NSL

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

PDB DOI: https://doi.org/10.2210/pdb5NSL/pdb

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

Deposited: 2017-04-26 Released: 2018-11-07
Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 165.29 kDa
Atom Count: 12,353
Modelled Residue Count: 1,248
Deposited Residue Count: 1,330
Unique protein chains: 1

Macromolecules

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(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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	9		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain G Interactions & Density Focus chain C Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 3
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 Interactions & Density Focus chain E Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	7		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G92805XC GlyCosmos: G92805XC GlyGen: G92805XC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AC [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SB [auth B] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VB [auth B] SDF format, chain WB [auth B] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain QB [auth B] SDF format, chain T [auth A] SDF format, chain UB [auth B] SDF format, chain XB [auth B] SDF format, chain YB [auth B] SDF format, chain ZB [auth B] MOL2 format, chain AC [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain ZB [auth B]	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		Interactions Focus chain AC [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AC [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B]
FRU Query on FRU Download Ideal Coordinates CCD File SDF format, chain BC [auth B] SDF format, chain W [auth A] MOL2 format, chain BC [auth B] MOL2 format, chain W [auth A]	BC [auth B], W [auth A]	beta-D-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-ARQDHWQXSA-N		Interactions Focus chain BC [auth B] Focus chain W [auth A] Interactions & Density Focus chain BC [auth B] Focus chain W [auth A]
975 Query on 975 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain CC [auth B] SDF format, chain DA [auth A] SDF format, chain DC [auth B] SDF format, chain EA [auth A] SDF format, chain EC [auth B] SDF format, chain FA [auth A] SDF format, chain FC [auth B] SDF format, chain GA [auth A] SDF format, chain GC [auth B] SDF format, chain HA [auth A] SDF format, chain HC [auth B] SDF format, chain IA [auth A] SDF format, chain IC [auth B] SDF format, chain JA [auth A] SDF format, chain JC [auth B] SDF format, chain KA [auth A] SDF format, chain KC [auth B] SDF format, chain LA [auth A] SDF format, chain LC [auth B] SDF format, chain MA [auth A] SDF format, chain MC [auth B] SDF format, chain NA [auth A] SDF format, chain NC [auth B] SDF format, chain OA [auth A] SDF format, chain OC [auth B] SDF format, chain PA [auth A] SDF format, chain PC [auth B] SDF format, chain QA [auth A] SDF format, chain QC [auth B] SDF format, chain RA [auth A] SDF format, chain RC [auth B] SDF format, chain SA [auth A] SDF format, chain SC [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DC [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FC [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GC [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain KC [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain LC [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain MC [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain NC [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain OC [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain PC [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain QC [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain RC [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain SC [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	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		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] Focus chain EA [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LC [auth B] Focus chain MA [auth A] Focus chain MC [auth B] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain OA [auth A] Focus chain OC [auth B] Focus chain PA [auth A] Focus chain PC [auth B] Focus chain QA [auth A] Focus chain QC [auth B] Focus chain RA [auth A] Focus chain RC [auth B] Focus chain SA [auth A] Focus chain SC [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] Focus chain EA [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain LA [auth A] Focus chain LC [auth B] Focus chain MA [auth A] Focus chain MC [auth B] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain OA [auth A] Focus chain OC [auth B] Focus chain PA [auth A] Focus chain PC [auth B] Focus chain QA [auth A] Focus chain QC [auth B] Focus chain RA [auth A] Focus chain RC [auth B] Focus chain SA [auth A] Focus chain SC [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain AD [auth B] SDF format, chain BB [auth A] SDF format, chain BD [auth B] SDF format, chain CB [auth A] SDF format, chain CD [auth B] SDF format, chain DB [auth A] SDF format, chain DD [auth B] SDF format, chain EB [auth A] SDF format, chain ED [auth B] SDF format, chain FB [auth A] SDF format, chain FD [auth B] SDF format, chain GB [auth A] SDF format, chain GD [auth B] SDF format, chain HB [auth A] SDF format, chain HD [auth B] SDF format, chain IB [auth A] SDF format, chain ID [auth B] SDF format, chain JB [auth A] SDF format, chain JD [auth B] SDF format, chain KB [auth A] SDF format, chain KD [auth B] SDF format, chain LB [auth A] SDF format, chain LD [auth B] SDF format, chain MB [auth A] SDF format, chain NB [auth A] SDF format, chain OB [auth A] SDF format, chain PB [auth A] SDF format, chain TA [auth A] SDF format, chain TC [auth B] SDF format, chain UA [auth A] SDF format, chain UC [auth B] SDF format, chain VA [auth A] SDF format, chain VC [auth B] SDF format, chain WA [auth A] SDF format, chain WC [auth B] SDF format, chain XA [auth A] SDF format, chain XC [auth B] SDF format, chain YA [auth A] SDF format, chain YC [auth B] SDF format, chain ZA [auth A] SDF format, chain ZC [auth B] MOL2 format, chain AB [auth A] MOL2 format, chain AD [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain BD [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain CD [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain DD [auth B] MOL2 format, chain EB [auth A] MOL2 format, chain ED [auth B] MOL2 format, chain FB [auth A] MOL2 format, chain FD [auth B] MOL2 format, chain GB [auth A] MOL2 format, chain GD [auth B] MOL2 format, chain HB [auth A] MOL2 format, chain HD [auth B] MOL2 format, chain IB [auth A] MOL2 format, chain ID [auth B] MOL2 format, chain JB [auth A] MOL2 format, chain JD [auth B] MOL2 format, chain KB [auth A] MOL2 format, chain KD [auth B] MOL2 format, chain LB [auth A] MOL2 format, chain LD [auth B] MOL2 format, chain MB [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain PB [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TC [auth B] MOL2 format, chain UA [auth A] MOL2 format, chain UC [auth B] MOL2 format, chain VA [auth A] MOL2 format, chain VC [auth B] MOL2 format, chain WA [auth A] MOL2 format, chain WC [auth B] MOL2 format, chain XA [auth A] MOL2 format, chain XC [auth B] MOL2 format, chain YA [auth A] MOL2 format, chain YC [auth B] MOL2 format, chain ZA [auth A] MOL2 format, chain ZC [auth B]	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		Interactions Focus chain AB [auth A] Focus chain AD [auth B] Focus chain BB [auth A] Focus chain BD [auth B] Focus chain CB [auth A] Focus chain CD [auth B] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FB [auth A] Focus chain FD [auth B] Focus chain GB [auth A] Focus chain GD [auth B] Focus chain HB [auth A] Focus chain HD [auth B] Focus chain IB [auth A] Focus chain ID [auth B] Focus chain JB [auth A] Focus chain JD [auth B] Focus chain KB [auth A] Focus chain KD [auth B] Focus chain LB [auth A] Focus chain LD [auth B] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth A] Focus chain TA [auth A] Focus chain TC [auth B] Focus chain UA [auth A] Focus chain UC [auth B] Focus chain VA [auth A] Focus chain VC [auth B] Focus chain WA [auth A] Focus chain WC [auth B] Focus chain XA [auth A] Focus chain XC [auth B] Focus chain YA [auth A] Focus chain YC [auth B] Focus chain ZA [auth A] Focus chain ZC [auth B] Interactions & Density Focus chain AB [auth A] Focus chain AD [auth B] Focus chain BB [auth A] Focus chain BD [auth B] Focus chain CB [auth A] Focus chain CD [auth B] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FB [auth A] Focus chain FD [auth B] Focus chain GB [auth A] Focus chain GD [auth B] Focus chain HB [auth A] Focus chain HD [auth B] Focus chain IB [auth A] Focus chain ID [auth B] Focus chain JB [auth A] Focus chain JD [auth B] Focus chain KB [auth A] Focus chain KD [auth B] Focus chain LB [auth A] Focus chain LD [auth B] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth A] Focus chain TA [auth A] Focus chain TC [auth B] Focus chain UA [auth A] Focus chain UC [auth B] Focus chain VA [auth A] Focus chain VC [auth B] Focus chain WA [auth A] Focus chain WC [auth B] Focus chain XA [auth A] Focus chain XC [auth B] Focus chain YA [auth A] Focus chain YC [auth B] Focus chain ZA [auth A] Focus chain ZC [auth B]

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 = 74.86	α = 90
b = 206.124	β = 90
c = 145.529	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: 2018-11-07

Deposition Author(s):

Ramirez-Escudero, M.

Sanz-Aparicio, J.

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