9KR9 | pdb_00009kr9

Overall structure of HKU5 S protein with S468A/Y463A mutation

PDB DOI: https://doi.org/10.2210/pdb9KR9/pdb
EM Map EMD-62523: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pipistrellus bat coronavirus HKU5
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-11-27 Released: 2025-11-05
Deposition Author(s): Zhang, Y.Y., Xia, L.Y., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5

Zhang, Y.Y., Xia, L.Y., Zhou, Q.

To be published.

Macromolecule Content

Total Structure Weight: 468.59 kDa
Atom Count: 28,851
Modeled Residue Count: 3,552
Deposited Residue Count: 4,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B [auth C], C [auth B]	1,352	Pipistrellus bat coronavirus HKU5	Mutation(s): 2 Gene Names: S, 2
UniProt
Find proteins for A3EXD0 (Bat coronavirus HKU5) Explore A3EXD0 Go to UniProtKB: A3EXD0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3EXD0
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth B]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, F, H, I, J, K, L, M, N, O, Q, R, S, T, U, V, W, X, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, P, Y	3		N-Glycosylation	Interactions Focus chain G Focus chain P Focus chain Y Interactions & Density Focus chain G Focus chain P Focus chain Y
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain EA [auth A] SDF format, chain AB [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain AB [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain AB [auth B]	AB [auth B], EA [auth A], PA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain EA [auth A] Focus chain PA [auth C] Interactions & Density Focus chain AB [auth B] Focus chain EA [auth A] Focus chain PA [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain OA [auth A] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KB [auth B] SDF format, chain KA [auth A] SDF format, chain JB [auth B] SDF format, chain JA [auth A] SDF format, chain IB [auth B] SDF format, chain IA [auth A] SDF format, chain HB [auth B] SDF format, chain HA [auth A] SDF format, chain GB [auth B] SDF format, chain GA [auth A] SDF format, chain FB [auth B] SDF format, chain FA [auth A] SDF format, chain EB [auth B] SDF format, chain DB [auth B] SDF format, chain CB [auth B] SDF format, chain BB [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain BB [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain BB [auth B]	BB [auth B] CB [auth B] DB [auth B] EB [auth B] FA [auth A] BB [auth B], CB [auth B], DB [auth B], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A], KB [auth B], LA [auth A], MA [auth A], NA [auth A], OA [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	G, P, Y	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain G Focus chain P Focus chain Y Interactions & Density Focus chain G Focus chain P Focus chain Y