SMTL ID : 8g77.1

SARS-CoV-2 spike/Nb6 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

11 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 A: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.4, R.8, N.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.124

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

NAG.12: 2 residues within 4Å: Chain A: I.1119, N.1121 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.318, T.320, Q.567 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: G.326, N.330 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: A.693, N.1061 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: G.59, T.60, N.61 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.151, N.152 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.109, T.111, V.114 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: T.95, N.221 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.95, N.221, T.223 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.318 Chain E: G.11 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: G.588, N.590, T.591 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.704, Q.913 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1061 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.4, N.124 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: S.58, G.59, T.60, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: E.119, N.151, N.152 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: N.109, A.110, T.111, N.112, V.114 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.109, T.111, N.112, F.144, F.162 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.318, T.320, Q.567, T.568 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: A.693, N.1061 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.4, N.124 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.151, N.152 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.330 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Dual-role epitope on SARS-CoV-2 spike enhances and neutralizes viral entry across different variants. Plos Pathog. (2024)

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
Nanosota-6: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
G

E
F

F
K

Spike glycoprotein

Nanosota-6

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