SMTL ID : 8vao.1

Simulation-driven design of prefusion stabilized SARS-CoV-2 spike S2 antigen

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.21, T.23, L.226, Q.230, Q.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.230 NAG.2: 3 residues within 4Å: Chain A: N.105, S.107, Q.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.105, A:S.107 NAG.3: 4 residues within 4Å: Chain A: N.402, G.403, H.405, F.407 No protein-ligand interaction detected (PLIP) NAG.4: 5 residues within 4Å: Chain B: N.21, T.23, L.226, Q.230, Q.375 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.230 NAG.5: 3 residues within 4Å: Chain B: N.105, S.107, Q.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.105, B:S.107 NAG.6: 4 residues within 4Å: Chain B: N.402, G.403, H.405, F.407 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain C: N.21, T.23, L.226, Q.230, Q.375 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.230 NAG.8: 3 residues within 4Å: Chain C: N.105, S.107, Q.108 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.105, C:S.107 NAG.9: 4 residues within 4Å: Chain C: N.402, G.403, H.405, F.407 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuqui, X. et al., Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nat Commun (2024)

Release Date

2024-07-10

Peptides

Spike protein S2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S2