SMTL ID : 7tl9.1

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

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

NAG-NAG.1: 2 residues within 4Å: Chain A: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: P.327, N.328, P.576, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: S.701, A.703, E.1069, K.1070, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.701 NAG-NAG.14: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1098 NAG-NAG.15: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

2 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.7: 3 residues within 4Å: Chain A: A.703, N.1071 Chain B: Q.892 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.12: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: D.336, F.339, N.340, L.368, P.370, F.371 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.613, T.615 Chain B: K.832 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: E.130, F.131, N.160 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: S.705, N.706, N.707 Chain B: Y.793 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain A: T.106, N.231, T.233 Chain C: S.456, L.458, E.462 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.120, T.122, N.123, V.125, V.166 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain C: Q.113, V.128, E.130, N.160, T.162 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.120, T.122, V.125, V.166 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: D.336, F.339, N.340, L.368 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.1131 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

2022-02-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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