SMTL ID : 8zby.1

SARS-CoV-2 Omicron BA.1 spike trimer (x2-4P) in complex with 3 D1F6 Fabs (0 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: 4 residues within 4Å: Chain A: N.697, L.902, Q.906, Q.1051 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.906 NAG-NAG.2: 2 residues within 4Å: Chain A: K.775, N.781 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1112, N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: N.697, L.902, Q.906, Q.1051 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: N.781, S.783 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain G: N.697, L.902, Q.906, Q.1051 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Q.906 NAG-NAG.10: 3 residues within 4Å: Chain G: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain G: I.1112, V.1113, N.1114 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.93, N.218 Chain G: E.449 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.266 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.315, P.563, Q.564 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.600, Q.628, T.629, G.632 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.689 Chain D: Y.776 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: A.686, E.1052, K.1053, N.1054 Chain D: Q.875 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.327, L.355 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.449 Chain D: N.218 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: E.265, N.266 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: N.315, P.563, Q.564 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.600, Q.628, T.629, G.632 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.689 Chain G: Y.776 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: A.686, E.1052, N.1054 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.327, L.355 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain G: N.218 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain G: N.266 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: N.315, P.563, Q.564 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain G: N.600, Q.628, T.629, G.632 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain G: N.689 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: Q.875 Chain G: A.686, E.1052, K.1053, N.1054 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.327, L.355 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep (2024)

Release Date

2024-05-15

Peptides

Spike glycoprotein: ADG
Heavy chain of D1F6 Fab: BEH
Light chain of D1F6 Fab: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
G

H
I

C
D

F
E

I
F

Spike glycoprotein

Heavy chain of D1F6 Fab

Light chain of D1F6 Fab

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