SMTL ID : 7mte.1

Structure of SARS-CoV-2 S2P spike at pH 7.4 refolded by low-pH treatment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

14 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.736, L.941, Q.945, Q.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: A.725, E.1091, N.1093 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.725 NAG-NAG.4: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.350, Q.599 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.736, L.941, Q.945 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.736, L.941, Q.945, Q.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.820, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.1153 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: N.299, N.301 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.299 Hydrogen bonds: A:N.299, A:N.301 NAG.16: 1 residues within 4Å: Chain A: N.635 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.635 NAG.17: 1 residues within 4Å: Chain A: N.676 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.676 NAG.18: 2 residues within 4Å: Chain A: N.728, G.1150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.728 NAG.19: 1 residues within 4Å: Chain B: N.80 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain B: E.300, N.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.301 NAG.21: 1 residues within 4Å: Chain B: N.635 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.635 NAG.22: 1 residues within 4Å: Chain B: N.676 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.676 NAG.23: 2 residues within 4Å: Chain B: N.728 Chain C: D.815 No protein-ligand interaction detected (PLIP) NAG.24: 4 residues within 4Å: Chain B: A.725, E.1091, K.1092, N.1093 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1093 NAG.25: 2 residues within 4Å: Chain C: E.300, N.301 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.299, C:N.301 NAG.26: 2 residues within 4Å: Chain C: N.635, T.637 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain C: N.728, I.1149, G.1150 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.1149 Hydrogen bonds: C:N.728 NAG.28: 3 residues within 4Å: Chain C: A.725, E.1091, N.1093 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olia, A.S. et al., SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity. J.Biol.Chem. (2021)

Release Date

2021-09-15

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein