9OW3 | pdb_00009ow3

Hedgehog coronavirus ErinCoV-12-19 spike receptor binding domain in complex with hedgehog APN (locally refined)

PDB DOI: https://doi.org/10.2210/pdb9OW3/pdb
EM Map EMD-70927: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Erinaceus europaeus, Streptomyces, Betacoronavirus Erinaceus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-02 Released: 2026-07-08
Deposition Author(s): Jin, M., Rini, J.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.01 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

Hedgehog coronavirus ErinCoV-12-19 spike receptor binding domain in complex with hedgehog APN (locally refined)

Jin, M., Rini, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 131.09 kDa
Atom Count: 9,357
Modeled Residue Count: 1,112
Deposited Residue Count: 1,113
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A	900	Erinaceus europaeus	Mutation(s): 0 Gene Names: ANPEP EC: 3.4.11
UniProt
Find proteins for A0A1S2ZAK1 (Erinaceus europaeus) Explore A0A1S2ZAK1 Go to UniProtKB: A0A1S2ZAK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S2ZAK1
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amastatin	B	4	Streptomyces	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C	209	Betacoronavirus Erinaceus	Mutation(s): 0
UniProt
Find proteins for U5LMM7 (Betacoronavirus Erinaceus/VMC/DEU/2012) Explore U5LMM7 Go to UniProtKB: U5LMM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5LMM7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File 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 C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] 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 C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] 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 C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	J [auth A] K [auth A] M [auth A] N [auth A] O [auth C] J [auth A], K [auth A], M [auth A], N [auth A], O [auth C], P [auth C], Q [auth C], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]