SMTL ID : 8uuo.1

Prototypic SARS-CoV-2 spike (containing V417) in the open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-MAN.1: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.801, C:S.803, C:Q.804 NAG-MAN.2: 2 residues within 4Å: Chain A: N.717, L.922 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.717, A:N.717 NAG-MAN.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1100

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.4: 1 residues within 4Å: Chain A: N.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.282 NAG.5: 1 residues within 4Å: Chain A: N.1074 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1074 NAG.6: 1 residues within 4Å: Chain A: N.801 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.709, G.1131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.709 NAG.9: 1 residues within 4Å: Chain B: N.1134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1134 NAG.10: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1098 NAG.11: 2 residues within 4Å: Chain B: K.1073, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.895 NAG.12: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.801, B:N.801, B:Q.804 NAG.13: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain B: N.616, T.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.616, B:T.618 NAG.15: 1 residues within 4Å: Chain B: N.709 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.709 NAG.17: 1 residues within 4Å: Chain C: N.709 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.709 NAG.18: 1 residues within 4Å: Chain C: N.616 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.616 NAG.19: 1 residues within 4Å: Chain C: N.1134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1134

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.16: 2 residues within 4Å: Chain C: N.717, L.922 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.717, C:N.717

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, Q. et al., Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. Elife (2023)

Release Date

2023-11-29

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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