SMTL ID : 7tgx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-MAN.1: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.790 NAG-MAN.2: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-MAN.3: 2 residues within 4Å: Chain B: N.704, L.909 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.913 NAG-MAN.4: 2 residues within 4Å: Chain B: N.1085, T.1087 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1087

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

NAG.5: 4 residues within 4Å: Chain A: N.267, E.268, N.269 Chain C: K.545 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.1121 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.696, G.1118 Chain C: D.783 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.1085, T.1087, F.1090 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: E.1059, N.1061 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.704 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: K.545 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.318 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: S.695, N.696, N.697 Ligand excluded by PLIP

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.6: 1 residues within 4Å: Chain A: N.704 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.704

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
C

B
A

C
B

Spike glycoprotein

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