8Y6C | pdb_00008y6c

Norovirus GII.10 P domain and 2'-FL (powder)

PDB DOI: https://doi.org/10.2210/pdb8Y6C/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-02 Released: 2024-06-19
Deposition Author(s): Hansman, G., Tame, J.R.H., Kher, G., Pancera, M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.191 (Depositor), 0.196 (DCC)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Human milk oligosaccharide 2'-fucosyllactose guards norovirus histo-blood group antigen co-factor binding site.

Rudd, P.A., Kher, G., Tame, J.R.H., Irie, H., Haselhorst, T., von Itzstein, M., Pancera, M., Hansman, G.S.

(2024) J Virol 98: e0086524-e0086524

PubMed: 38953656 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.00865-24
Primary Citation Related Structures:
8Y5V, 8Y6C, 8Y6D

Organizational Affiliation

Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.

Macromolecule Content

Total Structure Weight: 72.06 kDa
Atom Count: 5,681
Modeled Residue Count: 625
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GII.10 norovirus P domain in complex with 2'FL (powder)	A, B	315	Norovirus	Mutation(s): 0
UniProt
Find proteins for Q5F4T5 (Norwalk virus) Explore Q5F4T5 Go to UniProtKB: Q5F4T5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5F4T5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	C, D, E	3		N/A	Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G94133JU GlyCosmos: G94133JU GlyGen: G94133JU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain L [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain L [auth A]	CA [auth B], L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain L [auth A] Interactions & Density Focus chain CA [auth B] Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] F [auth A] G [auth A] H [auth A] AA [auth B], BA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]