7VHH

Delta variant of SARS-CoV-2 Spike protein

PDB DOI: https://doi.org/10.2210/pdb7VHH/pdb
EM Map EMD-31994: EMDB EMDataResource

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

Deposited: 2021-09-22 Released: 2022-12-28
Deposition Author(s): Liu, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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 delta variant SARS-CoV-2 Spike protein

Wang, X.

To be published.

Macromolecule Content

Total Structure Weight: 390.31 kDa
Atom Count: 25,795
Modelled Residue Count: 3,192
Deposited Residue Count: 3,405
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 [auth B], B [auth A], C	1,135	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 7 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 [auth B] Focus chain B [auth A] Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, E, F, G, H D, E, F, G, H, I, J, K, L, M, N, O	2		N-Glycosylation, O-Glycosylation	Interactions 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 Interactions & Density 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] 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 C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain P [auth B] SDF format, chain PA [auth C] SDF format, chain Q [auth B] SDF format, chain QA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain UA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] 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 C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain UA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] 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 C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain UA [auth C]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth C], NA [auth C], OA [auth C], P [auth B], PA [auth C], Q [auth B], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], 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 A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]