SMTL ID : 7tei.1

SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

11 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.1: 4 residues within 4Å: Chain A: N.798, S.800, Q.801, Q.932 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: S.701, A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain B: N.61, P.628 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: N.706, I.1127 Chain C: I.791, Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: E.130, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 2 residues within 4Å: Chain B: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain B: K.555 Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain C: N.120, T.122, N.123, V.125, V.166 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain C: F.335, D.336, F.339, N.340, V.364, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 1 residues within 4Å: Chain A: N.160 No protein-ligand interaction detected (PLIP)

8 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.3: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 6 residues within 4Å: Chain B: N.714, K.918, L.919, N.922, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.28: 5 residues within 4Å: Chain C: N.798, S.800, Q.801, K.808, F.814 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.33: 4 residues within 4Å: Chain A: N.714, L.919, N.922, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 Hydrogen bonds: A:N.922

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

NAG-NAG.4: 2 residues within 4Å: Chain B: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.600 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.654 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.120, T.122, N.123, V.125 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain A: N.613, T.615 Chain B: Y.834, G.835, D.836 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain A: S.456, N.457, L.458, K.459 Chain B: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: R.354 Chain C: Q.113, E.130, N.160, C.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.354, B:R.354 NAG-NAG.22: 4 residues within 4Å: Chain C: N.328, Q.577, T.578, L.579 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.578, C:T.578, C:L.579 NAG-NAG.24: 2 residues within 4Å: Chain C: N.600, T.601 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.654 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain A: Q.892 Chain C: S.701, A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain A: N.600 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.340, L.368 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: T.106, T.112, N.231 Chain C: E.462, D.464 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain A: N.120, T.122, N.123, V.125, V.166 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: D.336, N.340, L.368 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100, Y.1107 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: G.229, I.230, N.231 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Structural diversity of the SARS-CoV-2 Omicron spike. Mol.Cell (2022)

Release Date

2022-02-16

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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