9KR8 | pdb_00009kr8

Overall structure of HKU5 S protein in closed conformation

PDB DOI: https://doi.org/10.2210/pdb9KR8/pdb
EM Map EMD-62522: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pipistrellus bat coronavirus HKU5
Expression System: Homo sapiens
Mutation(s): No

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: 2.39 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: 468.54 kDa
Atom Count: 28,356
Modeled Residue Count: 3,489
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, C	1,352	Pipistrellus bat coronavirus HKU5	Mutation(s): 0 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 Focus chain C
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], D, E, F, G, AA [auth a], D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain D Focus chain E Focus chain F Focus chain G 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 P 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 Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain D Focus chain E Focus chain F Focus chain G 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 P 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 Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA (Subject of Investigation/LOI) Query on OLA Download Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain NA [auth A] SDF format, chain BB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain BB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain BB [auth C]	BB [auth C], NA [auth A], OA [auth B]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain BB [auth C] Focus chain NA [auth A] Focus chain OA [auth B] Interactions & Density Focus chain BB [auth C] Focus chain NA [auth A] Focus chain OA [auth B]
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain CB [auth C] SDF format, chain BA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain BA [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain BA [auth A]	BA [auth A], CB [auth C], PA [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CB [auth C] Focus chain PA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain CB [auth C] Focus chain PA [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain YA [auth B] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain NB [auth C] SDF format, chain MB [auth C] SDF format, chain MA [auth A] SDF format, chain LB [auth C] SDF format, chain LA [auth A] SDF format, chain KB [auth C] SDF format, chain KA [auth A] SDF format, chain JB [auth C] SDF format, chain JA [auth A] SDF format, chain IB [auth C] SDF format, chain IA [auth A] SDF format, chain HB [auth C] SDF format, chain HA [auth A] SDF format, chain GB [auth C] SDF format, chain GA [auth A] SDF format, chain FB [auth C] SDF format, chain FA [auth A] SDF format, chain EB [auth C] SDF format, chain EA [auth A] SDF format, chain DB [auth C] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain AB [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain MA [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain AB [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain MA [auth A] mmCIF format, chain LB [auth C] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain JA [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain AB [auth B]	AB [auth B] CA [auth A] DA [auth A] DB [auth C] EA [auth A] AB [auth B], CA [auth A], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], JA [auth A], JB [auth C], KA [auth A], KB [auth C], LA [auth A], LB [auth C], MA [auth A], MB [auth C], NB [auth C], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]