11HO | pdb_000011ho

1332D4 Spike KP3.1.1 Complex

PDB DOI: https://doi.org/10.2210/pdb11HO/pdb
EM Map EMD-75698: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-02-24 Released: 2026-08-26
Deposition Author(s): Kizziah, J.L., Walter, M.R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.26 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

Emergence of neutralizing RBD antibodies following Omicron infection with limited activity against ancestral SARS-CoV-2

Piepenbrink, M.S., Ma, Y., Panjwani, S., Blake, A.R., Bell, A.M., Kizziah, J.L., Mahmoud, S.H., Ippolito, G.C., Erdmann, N.B., Goepfert, P.A., Martinez-Sobrido, L., Kobie, J.J., Walter, M.R.

(2026) iScience 29

DOI: https://doi.org/10.1016/j.isci.2026.117166

Macromolecule Content

Total Structure Weight: 468.53 kDa
Atom Count: 26,756
Modeled Residue Count: 3,325
Deposited Residue Count: 4,128
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1332D4 Heavy Chain	A [auth D]	240	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1332D4 Light Chain	B [auth E]	234	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 KP3.1.1 variant	C [auth A], D [auth B], E [auth C]	1,218	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth C]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	2		N-Glycosylation, O-Glycosylation	Interactions 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 Interactions & Density 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

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 Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] 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 B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] 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 B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] 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 B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth A], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]