SMTL ID : 7ws9.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

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

NAG.15: 3 residues within 4Å: Chain A: F.59, S.60, N.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.16: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.277, A:E.278, A:N.279, C:K.555 NAG.17: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.706 NAG.18: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.277, B:E.278 NAG.19: 2 residues within 4Å: Chain B: N.706 Chain C: I.791 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.706 NAG.20: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.793, C:N.706 NAG.21: 4 residues within 4Å: Chain D: N.35, T.37, E.39, Q.322 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.35, D:T.37, D:E.39, D:Q.322 NAG.22: 4 residues within 4Å: Chain D: K.8, N.72, T.74, V.75 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.72, D:T.74 NAG.23: 2 residues within 4Å: Chain D: Q.63, N.85 No protein-ligand interaction detected (PLIP) NAG.24: 3 residues within 4Å: Chain D: N.304, M.305, Q.307 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Q.307 Hydrogen bonds: D:N.304 NAG.25: 5 residues within 4Å: Chain D: F.267, N.414, E.415, I.418, W.576 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.267, D:E.415, D:I.418, D:W.576 NAG.26: 2 residues within 4Å: Chain D: S.402, N.528 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.402, D:S.402, D:N.528

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
Processed angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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