6S1T

Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with sucrose

PDB DOI: https://doi.org/10.2210/pdb6S1T/pdb

Classification: HYDROLASE
Organism(s): Schwanniomyces occidentalis
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2019-06-19 Released: 2021-04-28
Deposition Author(s): Jimenez-Ortega, E., Sanz-Aparicio, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.214
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 126.04 kDa
Atom Count: 9,342
Modelled Residue Count: 1,024
Deposited Residue Count: 1,070
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructofuranosidase	A, B	535	Schwanniomyces occidentalis	Mutation(s): 0 EC: 3.2.1.26
UniProt
Find proteins for E5D0X5 (Schwanniomyces occidentalis) Explore E5D0X5 Go to UniProtKB: E5D0X5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E5D0X5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	F, G	2		N/A	Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] N [auth B] H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B]	L [auth A], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	F, G	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G