SMTL ID : 7ad1.1

Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(One up trimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

10 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: 2 residues within 4Å: Chain A: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.11: 2 residues within 4Å: Chain A: N.709, G.1131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.709 NAG.12: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1074 NAG.13: 2 residues within 4Å: Chain B: E.281, N.282 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.281 Hydrogen bonds: B:N.282 NAG.14: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.1130 Hydrogen bonds: B:N.709 NAG.15: 2 residues within 4Å: Chain B: N.717, Q.926 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.926, B:Q.1071 NAG.16: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.1072 Hydrogen bonds: B:N.1074 NAG.17: 1 residues within 4Å: Chain C: N.331 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain C: G.339, F.342, N.343 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.342 Hydrogen bonds: C:N.343 NAG.19: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130, G.1131 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.1130 Hydrogen bonds: C:N.709, A:D.796 NAG.20: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.1072 Hydrogen bonds: C:N.1074

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juraszek, J. et al., Stabilizing the closed SARS-CoV-2 spike trimer. Nat Commun (2021)

Release Date

2020-11-04

Peptides

Spike glycoprotein,Envelope glycoprotein,Spike glycoprotein,Envelope glycoprotein,SARS-CoV-2 S protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Envelope glycoprotein,Spike glycoprotein,Envelope glycoprotein,SARS-CoV-2 S protein

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