SMTL ID : 8err.1

SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

1 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 B: Y.793, N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.120, A.121 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.160, T.162 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: G.229, I.230, N.231 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.340, V.364, L.368 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.706, N.707 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: Y.793, N.798, S.800, Q.801 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.1095, F.1100 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: I.1129, N.1131 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.120 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: F.335, N.340, V.364, N.367 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: Q.892 Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.1095, F.1100 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.17 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: T.29, N.61 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.120, A.121, T.122, V.125 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Y.348 Chain C: N.159, N.160 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: K.459 Chain C: N.231 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: F.335, D.336, N.340, V.364 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.600, T.601 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.706, N.707 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: Y.793, N.798, S.800 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: N.1095, G.1096, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y.J. et al., Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Science (2022)

Release Date

2022-10-26

Peptides

Spike glycoprotein: ABC
S2X324 heavy chain: DFH
S2X324 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
E

H
I

E
L

G
F

I
J

Spike glycoprotein

S2X324 heavy chain

S2X324 light chain

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