SMTL ID : 7wg6.1

Neutral Omicron Spike Trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: T.95, N.220, T.222 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.317, Q.566, L.568 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.568 NAG-NAG.3: 1 residues within 4Å: Chain A: N.703 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: A.692, S.697, N.1060 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1060 NAG-NAG.5: 3 residues within 4Å: Chain A: N.787, S.789, Q.790 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain A: R.443, K.444, S.445, K.448, E.451 Chain B: T.95, N.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.444 NAG-NAG.9: 2 residues within 4Å: Chain B: R.314, N.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.314, B:T.567 NAG-NAG.10: 2 residues within 4Å: Chain B: N.703, Q.912 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: A.692, N.1060 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.787, S.789, F.803 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.803 NAG-NAG.14: 1 residues within 4Å: Chain B: N.1120 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: S.445, K.448 Chain C: T.95, N.220, T.222 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.317, Q.566 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: N.703, L.908 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: A.692, N.1060 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.787, S.789 No protein-ligand interaction detected (PLIP)

5 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.6: 4 residues within 4Å: Chain A: N.1084, T.1086, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 1 residues within 4Å: Chain A: N.1120 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: N.1084, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain C: N.1084, T.1086, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 1 residues within 4Å: Chain C: N.1120 No protein-ligand interaction detected (PLIP)

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

NAG.22: 4 residues within 4Å: Chain A: N.109, A.110, T.111, N.112 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: C.2, V.3, N.4 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: D.325, F.328, N.329 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.589, T.590 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.643 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.602, Q.630 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.695 Chain B: Y.782 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.132, S.240 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: C.2, N.4, N.124 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: D.325, N.329, L.357 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.643 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.602, Q.630 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.695 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.109, A.110, N.112 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.4, N.124 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.329, V.353, L.354, L.357 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.589 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.641, N.643 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.602, Q.630 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: Y.782 Chain C: N.695 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell (2022)

Release Date

2022-05-18

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein