SMTL ID : 8yz6.1

SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

4 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.720, L.925, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: T.719, N.720, L.925 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: E.1075, N.1077 Chain C: Q.898 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.1101, T.1103, H.1104 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 3 residues within 4Å: Chain C: N.720, Q.929, Q.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.929

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

NAG.6: 2 residues within 4Å: Chain A: N.804, S.806 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.806 NAG.7: 6 residues within 4Å: Chain A: A.709, A.716, E.1075, K.1076, N.1077 Chain B: Q.898 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.898, A:N.1077 Hydrophobic interactions: A:A.716, A:E.1075 NAG.8: 4 residues within 4Å: Chain A: N.1101, T.1103, H.1104, F.1106 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.1103 Hydrogen bonds: A:N.1101, A:T.1103, A:H.1104 NAG.9: 2 residues within 4Å: Chain B: N.804, S.806 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.806 NAG.10: 4 residues within 4Å: Chain B: N.1101, T.1103, F.1106, Y.1113 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.1103 Hydrogen bonds: B:N.1101, B:T.1103, B:T.1103, B:Y.1113 NAG.11: 6 residues within 4Å: Chain B: D.342, F.345, N.346, V.370, L.374, F.377 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.345, B:L.374, B:F.377 Hydrogen bonds: B:N.346 NAG.12: 3 residues within 4Å: Chain C: N.804, S.806, Q.807 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.806

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog. (2024)

Release Date

2024-06-05

Peptides

Spike glycoprotein: ABC
Fab heavy chain of JH-8B: D
Fab light chain of JH-8B: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Fab heavy chain of JH-8B

Fab light chain of JH-8B

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