SMTL ID : 7y9s.1

Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.719 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.803 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.333, P.581, Q.582 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: F.340, D.341, N.345, V.369 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.719, L.924, Q.928 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.924 NAG-NAG.8: 2 residues within 4Å: Chain B: N.803, S.805 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: S.706, A.708, E.1074, N.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: K.560 Chain C: N.282, E.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.719, L.924, Q.928 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.803, S.805, Q.806 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.1100, H.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1136 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain A: Y.33, F.64, N.66 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: T.111, N.236 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.282, E.283, N.284 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.345, V.369, L.373 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.711 Chain B: I.796, Y.798 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.1074, K.1075, N.1076 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.125, V.130, K.132, F.157 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: N.125, A.126, T.127, M.153, S.155 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.282, E.283, N.284 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.333, Q.582 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.711 Chain C: I.796, Y.798 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.33, N.66 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.236 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain C: V.123, N.125, T.127, N.128, V.130 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: R.459, S.461, K.464 Chain C: T.111, N.236 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.333, Q.582 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: I.796, Y.798 Chain C: N.711 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: F.340, D.341, N.345 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: Y.33, N.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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