SMTL ID : 7wp9.1

SARS-CoV-2 Omicron Variant SPIKE trimer, all RBDs down

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.328, P.576, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.798, S.800, Q.801, F.814 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.814 NAG-NAG.3: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.279 NAG.9: 3 residues within 4Å: Chain A: N.613 Chain B: I.831, K.832 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.613, A:T.615 Hydrophobic interactions: B:I.831 NAG.10: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.793 NAG.11: 1 residues within 4Å: Chain A: N.1131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1131 NAG.12: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.555, B:N.277, B:E.278 NAG.13: 5 residues within 4Å: Chain B: N.613, T.615, Q.641 Chain C: I.831, K.832 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.831 Hydrogen bonds: B:T.615 NAG.14: 1 residues within 4Å: Chain B: N.1131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.1131, B:N.1131 NAG.15: 4 residues within 4Å: Chain B: N.706, I.1127 Chain C: I.791, Y.793 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.1127 Hydrogen bonds: B:N.706 NAG.16: 2 residues within 4Å: Chain B: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain B: K.555 Chain C: N.277, E.278, N.279 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.555, C:N.277, C:N.279 Hydrophobic interactions: C:E.278 NAG.18: 4 residues within 4Å: Chain A: I.831, K.832 Chain C: N.613, Q.641 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.831 Hydrogen bonds: A:K.832, C:Q.641 NAG.19: 2 residues within 4Å: Chain C: N.328, Q.577 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.328 NAG.20: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.793 NAG.21: 1 residues within 4Å: Chain C: N.1131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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