SMTL ID : 8h01.1

SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in class 2 conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

15 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 C: N.715, L.920, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.920 NAG-NAG.7: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.704 NAG-NAG.9: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.12: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: A.704, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.17: 3 residues within 4Å: Chain A: T.106, N.232, T.234 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.106 NAG.18: 3 residues within 4Å: Chain A: E.279, N.280 Chain B: K.556 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.279 Hydrophobic interactions: B:K.556 NAG.19: 2 residues within 4Å: Chain A: N.329, T.579 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.329 NAG.20: 2 residues within 4Å: Chain A: N.707 Chain C: Y.794 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.707 NAG.21: 2 residues within 4Å: Chain B: Y.28, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.28 NAG.22: 2 residues within 4Å: Chain B: T.106, N.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.232 NAG.23: 3 residues within 4Å: Chain B: E.279, N.280 Chain C: K.556 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:K.556 Hydrogen bonds: B:E.279 NAG.24: 2 residues within 4Å: Chain A: Y.794 Chain B: N.707 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.707 NAG.25: 1 residues within 4Å: Chain C: N.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.61 NAG.26: 2 residues within 4Å: Chain C: T.106, N.232 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.232 NAG.27: 3 residues within 4Å: Chain A: K.556 Chain C: E.279, N.280 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:E.279 Hydrogen bonds: C:N.280, A:K.556 NAG.28: 2 residues within 4Å: Chain C: N.329, Q.578 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.329, C:Q.578 NAG.29: 2 residues within 4Å: Chain B: Y.794 Chain C: N.707 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.707

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants. Commun Biol (2023)

Release Date

2023-04-12

Peptides

Spike glycoprotein: ABC
rabbit monoclonal antibody 1H1 Fab light chain: DFH
rabbit monoclonal antibody 1H1 Fab heavy 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

rabbit monoclonal antibody 1H1 Fab light chain

rabbit monoclonal antibody 1H1 Fab heavy chain

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