SMTL ID : 8k47.1

A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

13 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: 8 residues within 4Å: Chain D: D.339, E.340, F.342, N.343, V.367, L.368, N.370, F.371 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.367 Hydrogen bonds: D:V.367, D:N.370 NAG-NAG.2: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain D: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.925 NAG-NAG.7: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP)

24 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.14: 6 residues within 4Å: Chain B: K.113, T.114, Q.115, E.132, N.164, N.165 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: G.199, G.232, N.234 Chain C: H.519 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.616, T.618, E.619 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: Y.655, N.657 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709 Chain D: I.794, Y.796 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: A.706, A.713, E.1072, K.1073, N.1074 Chain D: Q.895 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain C: T.108, N.234, T.236 Chain D: E.465, R.466 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain C: N.30, F.59, S.60, N.61, W.258 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.280, E.281, N.282 Chain D: K.558 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.616, E.619, Q.644 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: I.794, Y.796 Chain C: N.709 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: G.232, I.233, N.234 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: N.61, W.258, T.259 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.603, T.604 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.616, T.618, E.619 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: Y.655, V.656, N.657 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: I.794, Y.796 Chain D: S.708, N.709 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, H. et al., A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains. MedComm (2020) (2023)

Release Date

2023-12-13

Peptides

nanobody Nb4: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
A

C
B

D
C

nanobody Nb4

Spike glycoprotein

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