SMTL ID : 8dt8.1

LM18/Nb136 bispecific tetra-nanobody immunoglobulin in complex with SARS-CoV-2-6P-Mut7 S protein (focused refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.580, A:Q.580 NAG.2: 2 residues within 4Å: Chain A: N.801, S.803 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.801, A:S.803 NAG.3: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.644 Hydrogen bonds: A:N.616, A:T.618 NAG.4: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.717, A:Q.926, A:Q.1071 NAG.5: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.342, A:L.368 NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.1100, A:T.1100, A:T.1100 NAG.7: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.717, D:Q.926, D:Q.1071 NAG.8: 4 residues within 4Å: Chain D: D.796, N.801, S.803, Q.804 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.796 Hydrogen bonds: D:S.803, D:Q.804 NAG.9: 2 residues within 4Å: Chain D: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.1103 Hydrogen bonds: D:N.1098, D:T.1100 NAG.11: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.717, E:Q.926, E:Q.1071 NAG.12: 4 residues within 4Å: Chain E: K.795, D.796, N.801, S.803 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.795 Hydrogen bonds: E:S.803 NAG.13: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.1100 Hydrogen bonds: E:T.1100, E:T.1100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misson Mindrebo, L. et al., Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-06-14

Peptides

Spike glycoprotein: ADE
LM18 nanobody: B
Nb136 nanobody: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

E
B

B
H

C
D

Spike glycoprotein

LM18 nanobody

Nb136 nanobody

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