SMTL ID : 7wz1.1

SARS-CoV-2 Omicron Spike trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: S.705, N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.714, Q.1068 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: N.231, T.233 Chain C: E.462 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.798 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: I.791, Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: E.462 Chain C: T.106, N.231, T.233 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.328, P.576, Q.577, T.578 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.798 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, W. et al., Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer. J.Virol. (2022)

Release Date

2022-07-27

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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