SMTL ID : 8tyl.1

Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.33, N.66 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.127, A.128, N.130, V.132 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.285, N.287 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.336, Q.585 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.348, S.376, S.378, L.446 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.608 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.621 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.662 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.714, G.1136 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: A.711, E.1077, N.1079 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.722, Q.1076 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.806, S.808, Q.809 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Y.33, N.66 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.239, T.241 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.285, N.287 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.336, Q.585 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: T.312, N.608 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.621, T.623 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.662 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.714, G.1136 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.722, Q.931, Q.1076 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: A.711, E.1077, N.1079 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.806, S.808, Q.809 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: Y.33, N.66 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.239 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.287 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.336, Q.585 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: F.343, G.344, N.348 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.608 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.621 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.662 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.714, N.715, G.1136 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: A.711, E.1077, N.1079 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.722, Q.1076 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.806, S.808, Q.809 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruch, E.M. et al., Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Sci Rep (2024)

Release Date

2024-02-07

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein