9OW4 | pdb_00009ow4

Hedgehog coronavirus ErinCoV-12-19 spike receptor binding domain in complex with hedgehog APN

PDB DOI: https://doi.org/10.2210/pdb9OW4/pdb
EM Map EMD-70928: 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: 2.03 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

Jin, M., Rini, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 262.18 kDa
Atom Count: 18,478
Modeled Residue Count: 2,224
Deposited Residue Count: 2,226
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, D	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 Focus chain D
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C, F	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 Focus chain F
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	G, H, I, J, M G, H, I, J, M, N, O, P	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P

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	K, Q	3		N-Glycosylation	Interactions Focus chain K Focus chain Q Interactions & Density Focus chain K Focus chain Q

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	L, R	3		N-Glycosylation	Interactions Focus chain L Focus chain R Interactions & Density Focus chain L Focus chain R

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 AA [auth C] SDF format, chain BA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain CA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain CA [auth D]	AA [auth C] BA [auth D] CA [auth D] EA [auth D] FA [auth D] AA [auth C], BA [auth D], CA [auth D], EA [auth D], FA [auth D], GA [auth F], HA [auth F], IA [auth F], JA [auth F], S [auth A], T [auth A], V [auth A], W [auth A], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain U [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain U [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain U [auth A]	DA [auth D], U [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain U [auth A] Interactions & Density Focus chain DA [auth D] Focus chain U [auth A]