SMTL ID : 7xiy.1

SARS-CoV-2 Omicron BA.3 variant spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 5 residues within 4Å: Chain A: N.711, L.916, N.919, Q.920, Q.1065 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.916, A:N.919 NAG-NAG.2: 2 residues within 4Å: Chain A: N.795, S.797 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1092, T.1094, H.1095, F.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.711, L.916, Q.1065 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.916 NAG-NAG.6: 2 residues within 4Å: Chain B: N.795, S.797 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1092, T.1094, H.1095, F.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.711, L.916, Q.920, Q.1065 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.916 NAG-NAG.10: 2 residues within 4Å: Chain C: N.795, S.797 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.1092, T.1094, H.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1128 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: E.275, N.276 Chain C: K.552 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.325, Q.574, T.575 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.597 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.610, E.613 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: Y.649, N.651 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.703 Chain B: I.788, Y.790 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1068 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: D.333, N.337, F.365 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: K.552 Chain B: E.275, N.276 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.325, Q.574, T.575 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.597 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.610, E.613 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.649, N.651 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.703 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1068 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: K.552 Chain C: N.276 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.325, Q.574, T.575 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.597 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.610, E.613, R.640 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.651 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: I.788 Chain C: N.703 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1068 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.337, F.365 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein