28UT | pdb_000028ut

Crystal structure of the Norovirus GII.4 P domain in complex with Lacto-N-fucopentaose I (LNFP I)

PDB DOI: https://doi.org/10.2210/pdb28UT/pdb

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

Deposited: 2026-02-20 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: 2.00 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Norovirus GII.4 P domain in complex with Lacto-N-fucopentaose I (LNFP I)

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: 139.51 kDa
Atom Count: 10,205
Modeled Residue Count: 1,223
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B, C, D	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
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	3		N/A	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	F	5		N/A	Interactions Focus chain F Interactions & Density Focus chain F

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SCN (Subject of Investigation/LOI) Query on SCN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth D]	H [auth A], L [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	I [auth A], J [auth B], K [auth C], M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.179 (Depositor), 0.188 (DCC)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.581	α = 90
b = 128.198	β = 93.078
c = 102.701	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