5ZV7

P domain of GII.17-2014/15 complexed with B-trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb5ZV7/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus GII.17
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-05-09 Released: 2018-10-03 
• Deposition Author(s): Chen, Y., Li, X.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.93 kDa 
• Atom Count: 5,341 
• Modelled Residue Count: 611 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	309	Norovirus GII.17	Mutation(s): 0
UniProt
Find proteins for A0A0E3X5I8 (Norovirus GII.17) Explore A0A0E3X5I8  Go to UniProtKB:  A0A0E3X5I8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G11065GA GlyCosmos:  G11065GA GlyGen:  G11065GA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.699	α = 90
b = 86.851	β = 90
c = 97.431	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Chen, Y., Li, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670752

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-12-25
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary