9GXE | pdb_00009gxe

Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule

PDB DOI: https://doi.org/10.2210/pdb9GXE/pdb
EM Map EMD-51659: EMDB EMDataResource

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

Deposited: 2024-09-30 Released: 2025-03-26
Deposition Author(s): Drulyte, I., Pellegrino, S., Harman, M., Bezerra, G.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 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

Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule

Drulyte, I., Pellegrino, S., Harman, M., Bezerra, G.A.

To be published.

Macromolecule Content

Total Structure Weight: 391.08 kDa
Atom Count: 26,514
Modeled Residue Count: 3,300
Deposited Residue Count: 3,447
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,133	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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: 9	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Homotrimeric bicycle molecule	D, E, F	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 [auth AA], H [auth AB], I [auth AC], J [auth BA], K [auth BB], G [auth AA], H [auth AB], I [auth AC], J [auth BA], K [auth BB], L [auth BC], M [auth CA], N [auth CB], O [auth CC]	2		N-Glycosylation	Interactions Focus chain G [auth AA] Focus chain H [auth AB] Focus chain I [auth AC] Focus chain J [auth BA] Focus chain K [auth BB] Focus chain L [auth BC] Focus chain M [auth CA] Focus chain N [auth CB] Focus chain O [auth CC] Interactions & Density Focus chain G [auth AA] Focus chain H [auth AB] Focus chain I [auth AC] Focus chain J [auth BA] Focus chain K [auth BB] Focus chain L [auth BC] Focus chain M [auth CA] Focus chain N [auth CB] Focus chain O [auth CC]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain MA [auth C] SDF format, chain FA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain FA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain FA [auth B]	FA [auth B], MA [auth C], W [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain MA [auth C] Focus chain W [auth A] Interactions & Density Focus chain FA [auth B] Focus chain MA [auth C] Focus chain W [auth A]
KZ0 (Subject of Investigation/LOI) Query on KZ0 Download Ideal Coordinates CCD File SDF format, chain PA [auth F] SDF format, chain OA [auth E] SDF format, chain NA [auth D] MOL2 format, chain PA [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth D] mmCIF format, chain PA [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth D]	NA [auth D], OA [auth E], PA [auth F]	2,4,6-tris(chloromethyl)-1,3,5-triazine C₆ H₆ Cl₃ N₃ RICRAVHJCLFPFF-UHFFFAOYSA-N		Interactions Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F] Interactions & Density Focus chain NA [auth D] Focus chain OA [auth E] Focus chain PA [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain GA [auth C] SDF format, chain P [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain EA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth B], Y [auth B], 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 B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]