SMTL ID : 8g73.1

SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 bound at 2.5 A

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

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

NAG.12: 1 residues within 4Å: Chain B: N.269 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain B: G.326, F.329, N.330, V.354, L.355 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.603, Q.631 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: T.95, N.221 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.48 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: T.95, N.221, T.223 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: K.545 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.696, G.1118 Chain E: D.783 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.704, N.906, L.909, Q.1058 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.48 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.267, E.268, N.269 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.603, T.605 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: H.642, V.643, N.644 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19. J.Virol. (2023)

Release Date

2024-01-24

Peptides

Nanosota-3: ADF
Spike glycoprotein: BCE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
C

F
F

B
A

C
B

E
D

Nanosota-3

Spike glycoprotein

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