SMTL ID : 8oyt.1

Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation

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 A: E.283, N.284 Chain C: K.560 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: S.1099, N.1100, G.1101, T.1102, H.1103, F.1105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1102 NAG-NAG.4: 5 residues within 4Å: Chain A: N.719, F.720, L.924, Q.928, Q.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: K.797, N.803, S.805, Q.806 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.806 NAG-NAG.6: 5 residues within 4Å: Chain B: N.803, F.804, S.805, Q.806, I.933 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.719, L.924, Q.928, Q.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: I.1134, N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: N.1100, G.1101, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.803, S.805, Q.806 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: T.718, N.719, F.720, N.921, L.924, Q.1073 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.711 Chain B: I.796, Y.798 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.798 NAG.14: 7 residues within 4Å: Chain A: A.708, S.713, A.715, E.1074, K.1075, N.1076 Chain B: Q.897 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.897 Hydrophobic interactions: A:N.1076 NAG.15: 4 residues within 4Å: Chain B: A.708, E.1074, K.1075, N.1076 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.1074 Hydrogen bonds: B:N.1076 NAG.16: 2 residues within 4Å: Chain B: I.1134, N.1136 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain B: N.711 Chain C: I.796, Y.798 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.711 NAG.18: 4 residues within 4Å: Chain A: K.560 Chain B: N.282, E.283, N.284 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.282, B:E.283 Hydrogen bonds: B:N.284 NAG.19: 3 residues within 4Å: Chain B: K.560 Chain C: E.283, N.284 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.283 Hydrogen bonds: C:E.283 NAG.20: 5 residues within 4Å: Chain A: I.796, Y.798 Chain C: Y.709, S.710, N.711 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.711 NAG.21: 5 residues within 4Å: Chain C: A.708, A.715, E.1074, K.1075, N.1076 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornish, K. et al., Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biology (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein,Fibritin: ABC
H6 nanobody: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
G

F
F

Spike glycoprotein,Fibritin

H6 nanobody

Related Entries With Identical Sequence