SMTL ID : 7ws8.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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 B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.2: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: A.703, E.1069, N.1071 Chain C: Q.892 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.703 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: 4 residues within 4Å: Chain C: N.714, L.919, 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: 4 residues within 4Å: Chain C: S.701, 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 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)

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

NAG.15: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.706 Chain B: I.791 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.706 Chain C: I.791 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: K.555 Chain C: E.278, N.279 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain D: N.35, T.37, E.39, N.40, Q.322 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain D: K.8, N.72, T.74, V.75 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: Q.63, Q.83, N.85, H.177 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: E.294, N.304, M.305 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: F.267, N.414, W.576 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: S.402, N.528 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: T.34, N.35, Q.322 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: K.8, N.72, T.74 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: Q.63, Q.83, N.85 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: E.294, N.304, M.305, W.310 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain E: F.267, N.414, E.415, I.418, W.576 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.528 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
Processed angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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