SMTL ID : 7xdk.1

Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7054 and BA7125 fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.692, L.897, Q.901, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.306, Q.555 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain F: N.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain F: N.692, L.897, Q.901, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain F: N.776, S.778 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain F: N.306, Q.555 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain K: N.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain K: N.692, L.897, Q.901 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain K: N.776, S.778, F.792 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:F.792 NAG-NAG.12: 2 residues within 4Å: Chain K: N.306, Q.555 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.1109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1109 NAG.14: 2 residues within 4Å: Chain A: N.684, G.1106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.684 NAG.15: 3 residues within 4Å: Chain A: A.681, E.1047, N.1049 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1049 NAG.16: 1 residues within 4Å: Chain A: N.632 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain F: N.1109 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain F: N.684, G.1106 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.684 NAG.19: 3 residues within 4Å: Chain F: A.681, E.1047, N.1049 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain F: N.632 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.632 NAG.21: 1 residues within 4Å: Chain K: N.1109 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.1109 NAG.22: 3 residues within 4Å: Chain F: D.771 Chain K: N.684, G.1106 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:N.684, F:D.771 NAG.23: 4 residues within 4Å: Chain K: A.681, E.1047, K.1048, N.1049 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:E.1047 Hydrogen bonds: K:N.1049 NAG.24: 2 residues within 4Å: Chain K: H.630, N.632 No protein-ligand interaction detected (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

Spike glycoprotein: AFK
BA7125 fab: BGL
BA7125 fab: CHM
BA7054 fab: DIN
BA7054 fab: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

K
C

B
F

G
K

L
L

C
G

H
J

M
M

D
D

I
H

N
N

E
E

J
I

O
O

Spike glycoprotein

BA7125 fab

BA7125 fab

BA7054 fab

BA7054 fab

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