3WQ5
beta-Primeverosidase in complex with disaccharide substrate-analog N-beta-primeverosylamidine, natural aglycone derivative
- PDB DOI: https://doi.org/10.2210/pdb3WQ5/pdb
- Classification: HYDROLASE
- Organism(s): Camellia sinensis
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2014-01-22 Released: 2014-04-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.192 
- R-Value Work: 0.170 
- R-Value Observed: 0.171 
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-primeverosidase | 507 | Camellia sinensis | Mutation(s): 0  EC: 3.2.1.149 | ||
UniProt | |||||
Find proteins for Q7X9A9 (Camellia sinensis) Explore Q7X9A9  Go to UniProtKB:  Q7X9A9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q7X9A9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
VPA Query on VPA | E [auth A], G [auth A], H [auth B] | 2-phenyl-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)ethylamidine C19 H28 N2 O9 SKGTWJNDCFMXKU-GZDQRYBESA-N | |||
NAG Query on NAG | F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.192 
- R-Value Work: 0.170 
- R-Value Observed: 0.171 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.965 | α = 90 |
b = 88.19 | β = 90 |
c = 195.612 | γ = 90 |
Software Name | Purpose |
---|---|
CrystalClear | data collection |
MOLREP | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-04-23  Deposition Author(s): Saino, H.
Revision History (Full details and data files)
- Version 1.0: 2014-04-23
Type: Initial release - Version 1.1: 2015-04-01
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary