SMTL ID : 8wgv.1

BA.2(S375) Spike (S6P)/hACE2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

3 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: 6 residues within 4Å: Chain D: K.313, S.420, I.421, D.543, S.545, N.546 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.313, D:K.313 NAG-NAG.2: 3 residues within 4Å: Chain E: D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain F: K.313, H.417, S.420, N.546 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.313, F:S.420

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

NAG.4: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.231 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: E.278, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: E.278, N.279 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.706, N.707 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.119, T.121, N.122 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: K.555 Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.798, S.800 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.322, M.323, T.324 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: N.432, W.594 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain D: Q.81, N.103, V.107 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: K.26, N.90, V.93 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.53, E.57 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.322, M.323, W.328 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.432, I.436, W.594 Ligand excluded by PLIP NAG.47: 6 residues within 4Å: Chain E: Q.81, Q.101, N.103, S.106, N.194, H.195 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.90, T.92 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain E: N.53, T.55, E.57, V.339, Q.340 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain F: N.322, T.324, Q.325, W.328 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: F.285, N.432 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain F: T.78, Q.81, Q.101, N.103, N.194 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain F: K.26, Q.89, N.90, L.91 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain F: N.53, T.55, Q.340 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, X. et al., The receptor binding domain of SARS-CoV-2 Omicron subvariants targets Siglec-9 to decrease its immunogenicity by preventing macrophage phagocytosis. Nat.Immunol. (2024)

Release Date

2024-02-28

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Angiotensin-converting enzyme 2

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