Download MendeleyStructural basis for GII.4 norovirus inhibition by human milk oligosaccharides.
Singh, B.K., Hansman, G.S.To be published.
5J3O
Protruding domain of GII.4 human norovirus NSW0514 in complex with 3-fucosyllactose (3FL)
- PDB DOI: https://doi.org/10.2210/pdb5J3O/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-03-31 Released: 2017-04-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.47 Å
- R-Value Free: 0.201
- R-Value Work: 0.172
- R-Value Observed: 0.173
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VP1 | 309 | Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for K4LM89 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU) Explore K4LM89 Go to UniProtKB: K4LM89 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | K4LM89 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FUC Query on FUC | F [auth A], J [auth B] | alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N |  | ||
| EDO Query on EDO | C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.47 Å
- R-Value Free: 0.201
- R-Value Work: 0.172
- R-Value Observed: 0.173
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.07 | α = 90 |
| b = 55.57 | β = 107.28 |
| c = 115.51 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-04-12 Deposition Author(s): Singh, B.K., Hansman, G.S.
Revision History (Full details and data files)
- Version 1.0: 2017-04-12
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
