SMTL ID : 8zc3.1

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

11 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 A: N.695, Q.904, S.907 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.779, S.781, Q.782 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.1076, G.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: V.102, N.104, N.107, V.109 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.695, L.900 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.900 NAG-NAG.6: 2 residues within 4Å: Chain B: N.779, S.781 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.313, Q.562 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.695, L.900, Q.904 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.779, S.781 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.1076, G.1077, F.1081 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1112 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: E.263, N.264 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.313, Q.562 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.585, T.586 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.598, T.600, R.628 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: F.625, Y.637, N.639 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.687 Chain C: I.772 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: E.1050, N.1052 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: I.1110, N.1112 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: Y.12, N.45, T.47 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.216 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: Y.12, T.13, N.45 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: T.90, N.216, T.218 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.263, N.264 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.598 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.687 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Q.873 Chain B: A.684, N.1052 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.1076, T.1078, F.1081 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1112 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.325, F.353 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.313, Q.562, L.564 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: Y.12, T.13, N.14, N.45 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: T.90, T.96, N.216, T.218 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.598, T.600 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.637, N.639 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: I.772, Y.774 Chain C: N.687 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: A.684, E.1050, K.1051, N.1052 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.325, F.353 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
D

F
M

G
N

E
E

H
Q

I
R

Spike glycoprotein

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab

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