SMTL ID : 7xdb.1

Cryo-EM structure of SARS-CoV-2 Omicron Spike protein in complex with BA7208 fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

11 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: 4 residues within 4Å: Chain F: N.1070, T.1072, H.1073, F.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain F: N.689, L.894, Q.898, Q.1043 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.894 NAG-NAG.3: 3 residues within 4Å: Chain F: N.773, S.775, Q.776 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain G: N.1070, T.1072, H.1073, F.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain G: N.689, L.894, Q.898, Q.1043 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.894 NAG-NAG.6: 3 residues within 4Å: Chain G: N.773, S.775, Q.776 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain G: D.311, F.314, N.315, V.339 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1070, T.1072, H.1073, F.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.689, L.894, Q.898, Q.1043 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.773, S.775, Q.776 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: F.310, D.311, N.315, N.342, L.343 No protein-ligand interaction detected (PLIP)

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

NAG.12: 1 residues within 4Å: Chain B: N.1106 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.681 Chain G: I.766, Y.768 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: A.678, E.1044, K.1045, N.1046 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.588, T.590, Q.616 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain F: N.1106 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: I.766, Y.768 Chain F: N.681 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain F: A.678, E.1044, N.1046 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain F: N.588 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain F: P.302, N.303, P.551, Q.552 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain G: N.1106 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain F: I.766, Y.768 Chain G: N.681 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain G: A.678, E.1044, K.1045, N.1046 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain G: N.588, T.590, E.591 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain B: R.429, S.431, N.432, E.437 Chain G: T.81, N.206, T.208 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: I.440 Chain G: N.134, N.135 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain G: Y.3, N.36 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Biparatopic antibody BA7208/7125 effectively neutralizes SARS-CoV-2 variants including Omicron BA.1-BA.5. Cell Discov (2023)

Release Date

2023-03-01

Peptides

BA7208 fab: AEH
Spike glycoprotein: BFG
BA7208 fab: CDI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
F

H
H

B
A

F
C

G
B

C
D

D
G

I
I

BA7208 fab

Spike glycoprotein

BA7208 fab