9KOD | pdb_00009kod

Neuraminidase of A/dairy cow/Minnesota/24_016288-003/2024 (dcMN24 N1) in complex with CAV-F6 Fab

PDB DOI: https://doi.org/10.2210/pdb9KOD/pdb
EM Map EMD-62473: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-11-20 Released: 2025-07-02
Deposition Author(s): Wang, X., Ge, J., Li, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Neuraminidase of A/dairy cow/Minnesota/24_016288-003/2024 (dcMN24 N1) in complex with CAV-F6 Fab

Wang, X., Ge, J., Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 273.23 kDa
Atom Count: 19,148
Modeled Residue Count: 2,468
Deposited Residue Count: 2,468
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B, C, D	387	Influenza A virus	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A0A8K1VZ50 (Influenza A virus) Explore A0A8K1VZ50 Go to UniProtKB: A0A8K1VZ50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8K1VZ50
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAV-F6 heavy chain	E, G, I, K	123	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CAV-F6 kappa chain	F, H, J, L	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	M [auth A] N [auth A] Q [auth B] R [auth B] U [auth C] M [auth A], N [auth A], Q [auth B], R [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	AA [auth D] BA [auth D] O [auth A] P [auth A] S [auth B] AA [auth D], BA [auth D], O [auth A], P [auth A], S [auth B], T [auth B], W [auth C], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C]