SMTL ID : 8zc4.1

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 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.104, T.106, V.109, E.151 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.695, T.697, L.900, Q.904 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1076, T.1078, H.1079, F.1081 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.313, Q.562, T.563 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.563 NAG-NAG.5: 5 residues within 4Å: Chain B: N.104, T.106, N.107, V.109, V.153 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.153 Hydrogen bonds: B:N.107 NAG-NAG.6: 4 residues within 4Å: Chain B: N.313, P.561, Q.562, L.564 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.695, L.900, N.903 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.903 NAG-NAG.8: 2 residues within 4Å: Chain B: N.779, Q.782 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1076, T.1078, H.1079, F.1081 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.695, L.900 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.779 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1076, G.1077, H.1079, F.1081 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.12, N.14, N.45 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.264 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.598, T.600, Q.626 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: S.686, N.687 Chain C: Y.774 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.779 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.1052 Chain C: Q.873 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1112 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: T.90, N.216, T.218 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.264 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.325, N.352, F.353 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.598, Q.626, R.628 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: I.772, Y.774 Chain B: S.686, N.687 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.1050, N.1052 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1112 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.262, N.264 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.313, Q.562 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.325, F.353 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.598, T.600, Q.626 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: Y.774 Chain C: N.687 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: A.684, E.1050, N.1052 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.14, F.43, N.45 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: I.1110, N.1112 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: ABC
Light chain of D1F6 Fab: DFG
Heavy chain of D1F6 Fab: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
G

F
M

G
N

E
H

H
Q

I
R

Spike glycoprotein

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab

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