SMTL ID : 7tl1.1

SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

4 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: 8 residues within 4Å: Chain A: K.455, S.456, K.459, E.462 Chain B: T.106, N.231, T.233, R.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.456, A:S.456 NAG-NAG.2: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: T.106, N.231, T.233 Chain C: R.454, K.455, S.456, N.457, K.459 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.455 NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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.4: 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

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

NAG.6: 2 residues within 4Å: Chain A: N.340, L.368 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.120, T.122, V.125 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: E.278, N.279 Chain C: N.553, K.554, K.555 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: F.131, N.160 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.714, F.715, Q.923, Q.1068 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.613, Q.641 Chain C: Q.833 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: R.454, E.462, D.464 Chain C: N.231, T.233 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain C: S.1094, N.1095, T.1097, H.1098, F.1100, Y.1107 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: Q.833 Chain C: N.613, T.615 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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