SMTL ID : 8xi6.1

SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

9 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: 3 residues within 4Å: Chain A: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.709, L.914, Q.918, Q.1063 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.914 NAG-NAG.6: 3 residues within 4Å: Chain B: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.709, L.914, Q.918, Q.1063 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.914 NAG-NAG.11: 3 residues within 4Å: Chain C: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.709, L.914, Q.918, Q.1063 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.914

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.4: 6 residues within 4Å: Chain A: N.326 Chain D: S.28, S.30, G.31, S.75, N.104 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.30, D:S.75 NAG-NAG-BMA-FUC.9: 6 residues within 4Å: Chain B: N.326 Chain F: S.28, S.30, G.31, S.75, N.104 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.30, F:S.75 NAG-NAG-BMA-FUC.14: 6 residues within 4Å: Chain C: N.326 Chain H: S.28, S.30, G.31, S.75, N.104 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.30, H:S.75

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 1 residues within 4Å: Chain A: N.1126 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 1 residues within 4Å: Chain B: N.1126 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 1 residues within 4Å: Chain C: N.1126 No protein-ligand interaction detected (PLIP)

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

NAG.16: 5 residues within 4Å: Chain A: A.698, E.1064, K.1065, N.1066 Chain B: Q.887 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.275, E.276, N.277 Chain C: K.553 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.611 Chain B: I.826 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.117, T.119, V.122 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.338, N.365, F.366 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.701 Chain B: Y.788 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain B: A.698, E.1064, K.1065, N.1066 Chain C: Q.887 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: K.553 Chain B: N.275, E.276, N.277 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.611 Chain C: I.826 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.117, T.119, V.122 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.338, N.365, F.366 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.701 Chain C: Y.788 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: Q.887 Chain C: A.698, E.1064, K.1065, N.1066 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: K.553 Chain C: N.275, E.276, N.277 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: I.826 Chain C: N.611 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.117, T.119, V.122 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.338, N.365, F.366 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: Y.788 Chain C: N.701 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishimaru, H. et al., Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein. J.Virol. (2024)

Release Date

2024-04-24

Peptides

Spike glycoprotein: ABC
MO11 heavy chain: DFH
MO11 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

Spike glycoprotein

MO11 heavy chain

MO11 light chain