28NP | pdb_000028np

Crystal structure of the Norovirus GII.4 P domain in complex with 3 sialyl fucosyllactose

PDB DOI: https://doi.org/10.2210/pdb28NP/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus GII.4-GII.P16
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-10 Released: 2026-11-11
Deposition Author(s): Pisapia, L., Varrot, A.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.200 (Depositor), 0.208 (DCC)
R-Value Work:
0.144 (Depositor), 0.157 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 28NP

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the Norovirus GII.4 P domain in complex with 3 sialyl fucosyllactose

Pisapia, L., Flatau, H.N., Lin, S., Khanzhin, N., Imberty, A., Fragai, M., Angulo, J., Varrot, A.

To be published.

Macromolecule Content

Total Structure Weight: 70.04 kDa
Atom Count: 5,551
Modeled Residue Count: 616
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	310	Norovirus GII.4-GII.P16	Mutation(s): 0 Gene Names: ORF2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose	C	4		N/A	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] J [auth B] K [auth B] L [auth B] D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	F [auth A], G [auth A], I [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.200 (Depositor), 0.208 (DCC)
R-Value Work: 0.144 (Depositor), 0.157 (DCC)

Diffraction Data:

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.917	α = 90
b = 100.231	β = 90
c = 130.475	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union (EU)	European Union	101072717

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release