5ANN
Structure of fructofuranosidase from Xanthophyllomyces dendrorhous
- PDB DOI: https://doi.org/10.2210/pdb5ANN/pdb
- Classification: HYDROLASE
- Organism(s): Phaffia rhodozyma
- Mutation(s): No 
- Deposited: 2015-09-07 Released: 2016-02-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.188 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
BETA-FRUCTOFURANOSIDASE | 665 | Phaffia rhodozyma | Mutation(s): 0  EC: 3.2.1.26 | ||
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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | I [auth A], LA [auth B], Y [auth A], Z [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.188 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.62 | α = 90 |
b = 205.18 | β = 90 |
c = 145.77 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2016-02-10  Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.
Revision History (Full details and data files)
- Version 1.0: 2016-02-10
Type: Initial release - Version 1.1: 2016-04-06
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary