SMTL ID : 8hc6.1

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.10, Q.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.10, A:Q.259, A:Q.259 NAG.2: 5 residues within 4Å: Chain A: F.17, D.18, F.21, N.22, L.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.21 NAG.3: 3 residues within 4Å: Chain D: Y.15, F.46, N.48 No protein-ligand interaction detected (PLIP) NAG.4: 6 residues within 4Å: Chain D: N.107, T.109, N.110, V.111, V.112, F.139 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.139 Hydrogen bonds: D:N.107, D:V.111 NAG.5: 1 residues within 4Å: Chain D: N.147 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain D: G.216, N.218 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain D: N.266 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants. Nat Commun (2023)

Release Date

2023-01-25

Peptides

Spike protein S1: A
Heavy chain of YB9-258 Fab: B
Light chain of YB9-258: C
Spike protein S1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

D
B

Spike protein S1

Heavy chain of YB9-258 Fab

Light chain of YB9-258

Spike protein S1

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