9GXG | pdb_00009gxg

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

PDB DOI: https://doi.org/10.2210/pdb9GXG/pdb
EM Map EMD-51660: 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: 1.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 403.54 kDa
Atom Count: 28,265
Modeled Residue Count: 3,398
Deposited Residue Count: 3,492
Unique protein chains: 3

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: 15	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Biparatopic bicycle molecule (14mer)	D, E, F	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Biparatopic bicycle molecule (15mer)	G, H, I	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: 4
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 CA], BA [auth CB], CA [auth CC], DA [auth CD], EA [auth CE], AA [auth CA], BA [auth CB], CA [auth CC], DA [auth CD], EA [auth CE], FA [auth CF], GA [auth CG], J [auth AA], K [auth AB], L [auth AC], M [auth AD], N [auth AE], O [auth AF], P [auth AG], Q [auth AH], R [auth BA], S [auth BB], T [auth BC], U [auth BD], V [auth BE], W [auth BF], X [auth BG], Y [auth BH], Z [auth BI]	2		N-Glycosylation	Interactions Focus chain AA [auth CA] Focus chain BA [auth CB] Focus chain CA [auth CC] Focus chain DA [auth CD] Focus chain EA [auth CE] Focus chain FA [auth CF] Focus chain GA [auth CG] Focus chain J [auth AA] Focus chain K [auth AB] Focus chain L [auth AC] Focus chain M [auth AD] Focus chain N [auth AE] Focus chain O [auth AF] Focus chain P [auth AG] Focus chain Q [auth AH] Focus chain R [auth BA] Focus chain S [auth BB] Focus chain T [auth BC] Focus chain U [auth BD] Focus chain V [auth BE] Focus chain W [auth BF] Focus chain X [auth BG] Focus chain Y [auth BH] Focus chain Z [auth BI] Interactions & Density Focus chain AA [auth CA] Focus chain BA [auth CB] Focus chain CA [auth CC] Focus chain DA [auth CD] Focus chain EA [auth CE] Focus chain FA [auth CF] Focus chain GA [auth CG] Focus chain J [auth AA] Focus chain K [auth AB] Focus chain L [auth AC] Focus chain M [auth AD] Focus chain N [auth AE] Focus chain O [auth AF] Focus chain P [auth AG] Focus chain Q [auth AH] Focus chain R [auth BA] Focus chain S [auth BB] Focus chain T [auth BC] Focus chain U [auth BD] Focus chain V [auth BE] Focus chain W [auth BF] Focus chain X [auth BG] Focus chain Y [auth BH] Focus chain Z [auth BI]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R06 (Subject of Investigation/LOI) Query on R06 Download Ideal Coordinates CCD File SDF format, chain JB [auth D] SDF format, chain KB [auth E] SDF format, chain LB [auth F] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth F] mmCIF format, chain JB [auth D] mmCIF format, chain KB [auth E] mmCIF format, chain LB [auth F]	JB [auth D], KB [auth E], LB [auth F]	1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone C₉ H₁₂ Cl₃ N₃ O₃ FIABSBGSWCLPPP-UHFFFAOYSA-N		Interactions Focus chain JB [auth D] Focus chain KB [auth E] Focus chain LB [auth F] Interactions & Density Focus chain JB [auth D] Focus chain KB [auth E] Focus chain LB [auth F]
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain IB [auth C] SDF format, chain PA [auth A] SDF format, chain XA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain PA [auth A] MOL2 format, chain XA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain PA [auth A] mmCIF format, chain XA [auth B]	IB [auth C], PA [auth A], XA [auth B]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain IB [auth C] Focus chain PA [auth A] Focus chain XA [auth B] Interactions & Density Focus chain IB [auth C] Focus chain PA [auth A] Focus chain XA [auth B]
KZ0 (Subject of Investigation/LOI) Query on KZ0 Download Ideal Coordinates CCD File SDF format, chain MB [auth G] SDF format, chain NB [auth H] SDF format, chain OB [auth I] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth H] MOL2 format, chain OB [auth I] mmCIF format, chain MB [auth G] mmCIF format, chain NB [auth H] mmCIF format, chain OB [auth I]	MB [auth G], NB [auth H], OB [auth I]	2,4,6-tris(chloromethyl)-1,3,5-triazine C₆ H₆ Cl₃ N₃ RICRAVHJCLFPFF-UHFFFAOYSA-N		Interactions Focus chain MB [auth G] Focus chain NB [auth H] Focus chain OB [auth I] Interactions & Density Focus chain MB [auth G] Focus chain NB [auth H] Focus chain OB [auth I]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HA [auth A] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HA [auth A], HB [auth C], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] 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 YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] 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 YA [auth C] Focus chain ZA [auth C]