9BNE | pdb_00009bne

SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist

PDB DOI: https://doi.org/10.2210/pdb9BNE/pdb
EM Map EMD-44725: EMDB EMDataResource

Classification: VIRAL PROTEIN/ANTAGONIST
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-05-02 Released: 2025-08-27
Deposition Author(s): Young, T.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist

Young, T., Williams, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 675.37 kDa
Atom Count: 40,071
Modeled Residue Count: 4,955
Deposited Residue Count: 5,904
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2	A, C, E	680	Homo sapiens	Mutation(s): 0 Gene Names: COL18A1, ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P39060 (Homo sapiens) Explore P39060 Go to UniProtKB: P39060
PHAROS: P39060 GTEx: ENSG00000182871
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P39060Q9BYF1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, D, F	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain B Focus chain D Focus chain F	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	G, H, I, J [auth K], K [auth L], G, H, I, J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth J]	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth J] Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth J]

Small Molecules

Ligands 1 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 B] SDF format, chain BA [auth B] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth D] DA [auth D] EA [auth D] AA [auth B], BA [auth B], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IA [auth D], JA [auth D], KA [auth D], LA [auth D], MA [auth D], NA [auth D], OA [auth F], PA [auth F], QA [auth F], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B]