SMTL ID : 7ws1.1

Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-4-4-mer

Ligands

18 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: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.343 Chain D: S.56 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.343, V.367 Chain H: S.56 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.56 NAG-NAG.9: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.16: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: S.112, N.164, N.165 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.280, N.282 Chain C: F.559 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.616, T.618, R.646 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Structures of Omicron spike complexes and implications for neutralizing antibody development. Cell Rep (2022)

Release Date

2022-06-01

Peptides

Spike glycoprotein: ABC
510A5 light chain: DFHJ
510A5 heavy chain: EGIK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

H
F

J
J

E
E

G
I

I
G

K
K

Spike glycoprotein

510A5 light chain

510A5 heavy chain

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