SMTL ID : 8k45.1

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-3-2-mer

Ligands

10 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 A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.11: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: G.598, N.600, T.601 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1071 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: Y.348 Chain B: N.159, N.160 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: S.456, K.459, E.462 Chain B: I.230, N.231 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.328, I.329 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: K.555 Ligand excluded by PLIP NAG.30: 7 residues within 4Å: Chain C: S.110, K.111, E.130, Q.132, S.157, N.159, N.160 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: T.106, I.230, N.231, T.233 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 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

Spike glycoprotein: ABC
Nb4 nanobody: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Nb4 nanobody

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