SMTL ID : 8g75.1

SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound

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: 2 residues within 4Å: Chain A: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.9: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: 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 A: N.269 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.318 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: G.326, N.330, V.354 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: T.101, N.221 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: T.95, N.221 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.603, T.605, R.633 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: T.703, N.704, L.909, Q.1058 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.48 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.267, N.269 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: 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

Spike glycoprotein: ABC
Nanosota-4: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
G

F
F

Spike glycoprotein

Nanosota-4

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