SMTL ID : 9au2.1

VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-mer

Ligands

10 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 E: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain E: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain F: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain F: N.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.918 NAG-NAG.5: 3 residues within 4Å: Chain F: N.1094, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain F: N.328, Q.576, L.578 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain G: N.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.918 NAG-NAG.8: 1 residues within 4Å: Chain F: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain G: N.242, S.244 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain E: N.713, Q.922, Q.1067 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain E: N.1130 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain E: N.279 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain E: N.612 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain E: N.705 Chain F: Y.792 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain E: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain E: N.340 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain E: N.351, T.353 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain E: N.653 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain E: N.599 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain E: F.60, N.62 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: N.328, P.575, Q.576 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain E: G.229, N.231 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain E: N.162, N.163 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain F: N.612, Q.640 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain F: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.279 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain F: Y.703, N.705 Chain G: Y.792 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain G: N.277, N.279 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: N.1094, H.1097, F.1099 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain G: N.231 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain G: N.121, F.126 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: N.328, Q.576 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: Y.792 Chain G: N.705 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain G: N.1130 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain G: N.163 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: F.60, N.62 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: A.702, N.1070 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.612, Q.640 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosen, L.E. et al., A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification. Cell (2024)

Release Date

2024-10-16

Peptides

VIR-7229 Fab heavy chain: AB
VIR-7229 Fab light chain: CD
Spike glycoprotein: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
I

D
J

E
A

F
B

G
C

VIR-7229 Fab heavy chain

VIR-7229 Fab light chain

Spike glycoprotein

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