SMTL ID : 8usz.1

Cryo-EM Structure of Full-Length Spike Protein of Omicron XBB.1.5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.1079, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.1079, H.1082 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.1079, H.1082, F.1084 No protein-ligand interaction detected (PLIP)

19 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.4: 2 residues within 4Å: Chain A: N.312, Q.561 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.597 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.690 Chain B: I.775, Y.777 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.698, L.903, Q.907 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.782, Q.785 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: A.687, K.1054, N.1055 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1115 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.597, T.599 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.690 Chain C: I.775, Y.777 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.698, L.903, Q.907 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.782, S.784 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: A.687, E.1053, N.1055 Chain C: Q.876 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.1115 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.597, Q.625 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: I.775, Y.777 Chain C: S.689, N.690 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.698, Q.907 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.782, S.784, Q.785 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: A.687, N.1055 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.1115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Modjarrad, K. et al., Preclinical characterization of the Omicron XBB.1.5-adapted BNT162b2 COVID-19 vaccine. Npj Vaccines (2024)

Release Date

2024-12-04

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein