SMTL ID : 8xki.1

A neutralizing nanobody VHH60 against wt SARS-CoV-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

6 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 D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: E.281, N.282 Chain D: K.558 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain B: A.706, S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, S.371 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain C: F.329, P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.709 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain D: N.709 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: K.113, Q.115, N.165 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: T.108, N.234, I.235 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.717, Q.926 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: Q.895 Chain D: A.713, K.1073, N.1074 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q. et al., A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug. Cell Death Dis (2024)

Release Date

2024-07-10

Peptides

nanobody VHH60: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

nanobody VHH60

Spike glycoprotein

Related Entries With Identical Sequence