SMTL ID : 7tge.1

SARS-CoV-2 Omicron 1-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

9 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: 4 residues within 4Å: Chain A: N.120, V.125, E.164, V.166 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.613, T.615 Chain B: I.831, G.835 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.714, F.715, L.919, N.922, Q.923 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.922, A:Q.923 NAG-NAG.4: 5 residues within 4Å: Chain A: N.798, S.800, Q.801, F.814, Q.932 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.801, A:F.814 NAG-NAG.5: 5 residues within 4Å: Chain A: C.1079, H.1080, G.1082, C.1123, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: S.456, N.457, E.462 Chain B: T.106, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: T.713, N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: E.278, N.279 Chain C: K.555 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: N.654, N.655 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.706 Chain B: I.791 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: T.106, N.231, T.233 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: S.110, E.130, F.131, N.160 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.706 Chain C: I.791 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: K.792, N.798, S.800 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: Q.113, E.130, N.160, T.162 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

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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