SMTL ID : 8k46.1

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-3-3-mer

Ligands

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

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

NAG.13: 4 residues within 4Å: Chain D: G.232, I.233, N.234 Chain E: H.519 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain D: N.61, G.257, W.258 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain D: N.280, E.281, N.282 Chain E: K.558 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: E.309, N.603, T.604 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain D: N.616, T.618, E.619, Q.644 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: Y.655, N.657 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.709 Chain F: I.794, Y.796 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain E: S.112, A.163, N.164 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain E: T.108, N.234, T.236 Chain F: R.466 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: N.30, N.61, W.258 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: N.280, E.281, N.282 Chain F: K.558 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain E: N.616, T.618, E.619, Q.644 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: Y.655, N.657 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: I.794, Y.796 Chain E: N.709 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: I.794, Y.796 Chain F: N.709 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain F: T.29, N.61, W.258, T.259 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: N.616, T.618, E.619 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain F: N.657 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain F: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain F: D.339, E.340, F.342, N.343, V.367, L.368, F.371 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: ABC
Spike glycoprotein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

C
I

D
A

E
B

F
C

nanobody Nb4

Spike glycoprotein

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