5IYR
Protruding domain of GII.4 human norovirus CHDC2094 in complex with 2-fucosyllactose (2'FL)
- PDB DOI: https://doi.org/10.2210/pdb5IYR/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Norovirus Hu/GII.4/CHDC2094/1974/US
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2016-03-24 Released: 2017-04-05 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.54 Å
- R-Value Free: 0.170 
- R-Value Work: 0.136 
- R-Value Observed: 0.138 
wwPDB Validation   3D Report Full Report
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 |
GII.4 norovirus CHDC2094 capsid | 306 | Norovirus Hu/GII.4/CHDC2094/1974/US | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for D0QJ68 (Norovirus Hu/GII.4/CHDC2094/1974/US) Explore D0QJ68  Go to UniProtKB:  D0QJ68 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | D0QJ68 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
FLC Query on FLC | E [auth B] | CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.54 Å
- R-Value Free: 0.170 
- R-Value Work: 0.136 
- R-Value Observed: 0.138 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 90.29 | α = 90 |
b = 106.47 | β = 90 |
c = 135.47 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-04-05  Deposition Author(s): Singh, B.K., Hansman, G.S.
Revision History (Full details and data files)
- Version 1.0: 2017-04-05
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: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary