SMTL ID : 7tgy.1

Prototypic SARS-CoV-2 G614 spike (closed form)

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.788, S.790, Q.791, Q.922 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.791, A:Q.922 NAG-NAG.2: 3 residues within 4Å: Chain A: N.1085, T.1087, H.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: N.704, F.705, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.913 NAG-NAG.4: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.603, T.605 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.693

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

NAG.10: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: G.326, N.330 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.267, E.268, N.269 Chain C: K.545 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.704, L.909, Q.1058 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1121 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.330, S.358, S.360 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.603, T.605, Q.631 Chain C: I.821 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1061 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1121 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: E.452 Chain C: T.95, N.221 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: K.545 Chain C: N.267, E.268, N.269 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.1085, H.1088 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain. Nat Commun (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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