SMTL ID : 7xdl.1

Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7208 and BA7125 fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.08 Å

Oligo State

hetero-3-3-3-3-3-mer

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: 4 residues within 4Å: Chain A: N.1071, T.1073, H.1074, F.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.690, L.895, Q.899, Q.1044 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.895 NAG-NAG.3: 3 residues within 4Å: Chain A: N.774, S.776, Q.777 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.304, Q.553 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1071, T.1073, H.1074, F.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.690, L.895, Q.899 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.774, S.776, Q.777 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.304, Q.553 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1071, T.1073, H.1074, F.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.690, L.895, Q.899, Q.1044 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.774, S.776 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.304, Q.553 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.1107 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: N.682, G.1104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.682 NAG.15: 3 residues within 4Å: Chain A: A.679, E.1045, N.1047 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1047 NAG.16: 1 residues within 4Å: Chain A: N.630 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.630 NAG.17: 1 residues within 4Å: Chain B: N.1107 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain B: N.682, G.1104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.682 NAG.19: 3 residues within 4Å: Chain B: A.679, E.1045, N.1047 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1047 NAG.20: 1 residues within 4Å: Chain B: N.630 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.630 NAG.21: 1 residues within 4Å: Chain C: N.1107 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1107 NAG.22: 3 residues within 4Å: Chain B: D.769 Chain C: N.682, G.1104 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.682 NAG.23: 4 residues within 4Å: Chain C: A.679, E.1045, K.1046, N.1047 No protein-ligand interaction detected (PLIP) NAG.24: 1 residues within 4Å: Chain C: N.630 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.630

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

2023-03-15

Peptides

Spike glycoprotein: ABC
BA7125 fab: DFH
BA7125 fab: EGI
BA7208 fab: JLN
BA7208 fab: KMO

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

J
J

L
L

N
O

K
K

M
M

O
P

Spike glycoprotein

BA7125 fab

BA7125 fab

BA7208 fab

BA7208 fab