SMTL ID : 7qo7.1

SARS-CoV-2 S Omicron Spike B.1.1.529

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: N.120, A.121, N.123, V.125, F.152 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.706 Chain C: I.791, Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

18 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: C.134, N.135, R.153 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 1 residues within 4Å: Chain A: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA.9: 2 residues within 4Å: Chain A: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain B: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.714, L.919 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA.13: 3 residues within 4Å: Chain A: Y.793 Chain B: N.706, I.1127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain B: N.279 Chain C: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain B: I.791, Y.793 Chain C: N.706 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.791 NAG-NAG-BMA.20: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 2 residues within 4Å: Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.22: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.24: 4 residues within 4Å: Chain A: T.106, N.231, T.233 Chain B: E.462 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.462 NAG.25: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 No protein-ligand interaction detected (PLIP) NAG.26: 2 residues within 4Å: Chain A: N.328, Q.577 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.328, A:Q.577 NAG.27: 4 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain C: G.835 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.613, A:E.616 NAG.28: 1 residues within 4Å: Chain A: N.654 No protein-ligand interaction detected (PLIP) NAG.29: 5 residues within 4Å: Chain A: I.831, D.836 Chain B: N.613, T.615, E.616 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.615 NAG.30: 2 residues within 4Å: Chain B: N.328, Q.577 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.328 NAG.31: 2 residues within 4Å: Chain B: Y.652, N.654 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.654 NAG.32: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1071 NAG.33: 2 residues within 4Å: Chain B: F.59, N.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.61 NAG.34: 1 residues within 4Å: Chain C: N.600 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.600 NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.28, C:N.61 NAG.36: 4 residues within 4Å: Chain B: Y.834 Chain C: N.613, T.615, Q.641 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.641, B:Y.834 Hydrogen bonds: C:N.613 NAG.37: 1 residues within 4Å: Chain C: N.654 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, D. et al., Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion. Biorxiv (2021)

Release Date

2022-01-19

Peptides

Surface glycoprotein,Fibritin,SARS-CoV-2 S Omicron Spike B.1.1.529: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Surface glycoprotein,Fibritin,SARS-CoV-2 S Omicron Spike B.1.1.529

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