7WJZ

Omicron Spike bitrimer with 6m6 antibody

PDB DOI: https://doi.org/10.2210/pdb7WJZ/pdb
EM Map EMD-32553: EMDB EMDataResource

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

Deposited: 2022-01-08 Released: 2022-07-13
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 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.

Macromolecule Content

Total Structure Weight: 1,148.16 kDa
Atom Count: 69,158
Modelled Residue Count: 8,886
Deposited Residue Count: 10,356
Unique protein chains: 3

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] D [auth I] G [auth J] J [auth K] M [auth L] A [auth B], D [auth I], G [auth J], J [auth K], M [auth L], P [auth M]	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 39 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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 heavy chain	B [auth A] E [auth D] H [auth E] K [auth F] N [auth G] B [auth A], E [auth D], H [auth E], K [auth F], N [auth G], Q [auth H]	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 light chain	C F [auth N] I [auth O] L [auth P] O [auth Q] C, F [auth N], I [auth O], L [auth P], O [auth Q], R	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 PA [auth K] SDF format, chain AA [auth I] SDF format, chain AB [auth L] SDF format, chain BA [auth I] SDF format, chain BB [auth L] SDF format, chain CA [auth I] SDF format, chain CB [auth L] SDF format, chain DA [auth I] SDF format, chain DB [auth L] SDF format, chain EA [auth I] SDF format, chain EB [auth L] SDF format, chain FA [auth I] SDF format, chain FB [auth M] SDF format, chain GA [auth I] SDF format, chain GB [auth M] SDF format, chain HA [auth J] SDF format, chain HB [auth M] SDF format, chain IA [auth J] SDF format, chain IB [auth M] SDF format, chain JA [auth J] SDF format, chain JB [auth M] SDF format, chain KA [auth J] SDF format, chain KB [auth M] SDF format, chain LA [auth J] SDF format, chain LB [auth M] SDF format, chain MA [auth J] SDF format, chain MB [auth M] SDF format, chain NA [auth J] SDF format, chain NB [auth M] SDF format, chain OA [auth J] SDF format, chain OB [auth M] SDF format, chain QA [auth K] SDF format, chain RA [auth K] SDF format, chain S [auth B] SDF format, chain SA [auth K] SDF format, chain T [auth B] SDF format, chain TA [auth K] SDF format, chain U [auth B] SDF format, chain UA [auth K] SDF format, chain V [auth B] SDF format, chain VA [auth K] SDF format, chain W [auth B] SDF format, chain WA [auth L] SDF format, chain X [auth B] SDF format, chain XA [auth L] SDF format, chain Y [auth B] SDF format, chain YA [auth L] SDF format, chain Z [auth I] SDF format, chain ZA [auth L] MOL2 format, chain PA [auth K] MOL2 format, chain AA [auth I] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth I] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth I] MOL2 format, chain CB [auth L] MOL2 format, chain DA [auth I] MOL2 format, chain DB [auth L] MOL2 format, chain EA [auth I] MOL2 format, chain EB [auth L] MOL2 format, chain FA [auth I] MOL2 format, chain FB [auth M] MOL2 format, chain GA [auth I] MOL2 format, chain GB [auth M] MOL2 format, chain HA [auth J] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth J] MOL2 format, chain IB [auth M] MOL2 format, chain JA [auth J] MOL2 format, chain JB [auth M] MOL2 format, chain KA [auth J] MOL2 format, chain KB [auth M] MOL2 format, chain LA [auth J] MOL2 format, chain LB [auth M] MOL2 format, chain MA [auth J] MOL2 format, chain MB [auth M] MOL2 format, chain NA [auth J] MOL2 format, chain NB [auth M] MOL2 format, chain OA [auth J] MOL2 format, chain OB [auth M] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth K] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth L] MOL2 format, chain Z [auth I] MOL2 format, chain ZA [auth L]	AA [auth I] AB [auth L] BA [auth I] BB [auth L] CA [auth I] AA [auth I], AB [auth L], BA [auth I], BB [auth L], CA [auth I], CB [auth L], DA [auth I], DB [auth L], EA [auth I], EB [auth L], FA [auth I], FB [auth M], GA [auth I], GB [auth M], HA [auth J], HB [auth M], IA [auth J], IB [auth M], JA [auth J], JB [auth M], KA [auth J], KB [auth M], LA [auth J], LB [auth M], MA [auth J], MB [auth M], NA [auth J], NB [auth M], OA [auth J], OB [auth M], PA [auth K], QA [auth K], RA [auth K], S [auth B], SA [auth K], T [auth B], TA [auth K], U [auth B], UA [auth K], V [auth B], VA [auth K], W [auth B], WA [auth L], X [auth B], XA [auth L], Y [auth B], YA [auth L], Z [auth I], ZA [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth I] Focus chain AB [auth L] Focus chain BA [auth I] Focus chain BB [auth L] Focus chain CA [auth I] Focus chain CB [auth L] Focus chain DA [auth I] Focus chain DB [auth L] Focus chain EA [auth I] Focus chain EB [auth L] Focus chain FA [auth I] Focus chain FB [auth M] Focus chain GA [auth I] Focus chain GB [auth M] Focus chain HA [auth J] Focus chain HB [auth M] Focus chain IA [auth J] Focus chain IB [auth M] Focus chain JA [auth J] Focus chain JB [auth M] Focus chain KA [auth J] Focus chain KB [auth M] Focus chain LA [auth J] Focus chain LB [auth M] Focus chain MA [auth J] Focus chain MB [auth M] Focus chain NA [auth J] Focus chain NB [auth M] Focus chain OA [auth J] Focus chain OB [auth M] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain WA [auth L] Focus chain X [auth B] Focus chain XA [auth L] Focus chain Y [auth B] Focus chain YA [auth L] Focus chain Z [auth I] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth I] Focus chain AB [auth L] Focus chain BA [auth I] Focus chain BB [auth L] Focus chain CA [auth I] Focus chain CB [auth L] Focus chain DA [auth I] Focus chain DB [auth L] Focus chain EA [auth I] Focus chain EB [auth L] Focus chain FA [auth I] Focus chain FB [auth M] Focus chain GA [auth I] Focus chain GB [auth M] Focus chain HA [auth J] Focus chain HB [auth M] Focus chain IA [auth J] Focus chain IB [auth M] Focus chain JA [auth J] Focus chain JB [auth M] Focus chain KA [auth J] Focus chain KB [auth M] Focus chain LA [auth J] Focus chain LB [auth M] Focus chain MA [auth J] Focus chain MB [auth M] Focus chain NA [auth J] Focus chain NB [auth M] Focus chain OA [auth J] Focus chain OB [auth M] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth B] Focus chain SA [auth K] Focus chain T [auth B] Focus chain TA [auth K] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth B] Focus chain WA [auth L] Focus chain X [auth B] Focus chain XA [auth L] Focus chain Y [auth B] Focus chain YA [auth L] Focus chain Z [auth I] Focus chain ZA [auth L]