SMTL ID : 7ws5.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

14 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 C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: Q.892 Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.12: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: N.30, N.61 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain A: N.277, N.279 Chain B: K.555 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.555, A:N.279 NAG.17: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: E.278, N.279 Chain C: K.555 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.278 NAG.19: 2 residues within 4Å: Chain B: N.328, Q.577 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.328 NAG.20: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.706 NAG.21: 1 residues within 4Å: Chain C: N.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.231 NAG.22: 2 residues within 4Å: Chain C: E.278, N.279 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.278, C:N.279 NAG.23: 2 residues within 4Å: Chain C: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain B: I.791 Chain C: N.706 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.706

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: DFH
510A5 heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

Spike glycoprotein

510A5 light chain

510A5 heavy chain

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