SMTL ID : 8hc7.1

SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fab, focused refinement of RBD-dimer 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: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 No protein-ligand interaction detected (PLIP) NAG.2: 6 residues within 4Å: Chain A: N.107, T.109, N.110, V.111, V.112, F.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.139 Hydrogen bonds: A:N.107, A:V.111 NAG.3: 2 residues within 4Å: Chain A: N.146, N.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.146 NAG.4: 5 residues within 4Å: Chain A: N.218, T.220 Chain B: R.136, S.138, N.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.136, B:S.138, B:S.138 NAG.5: 1 residues within 4Å: Chain A: N.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.266 NAG.6: 3 residues within 4Å: Chain A: D.323, N.327, L.355 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: D.18, N.22, L.50 No protein-ligand interaction detected (PLIP)

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
Spike protein S1: B
Heavy chain variable region of YB9-258: C
Light chain variable region of YB9-258: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
H

D
L

Spike protein S1

Spike protein S1

Heavy chain variable region of YB9-258

Light chain variable region of YB9-258

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