SMTL ID : 8oyu.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

11 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: 2 residues within 4Å: Chain A: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: N.1095, G.1096, T.1097, H.1098, F.1100, Y.1107, P.1109, I.1111 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1100 NAG-NAG.3: 7 residues within 4Å: Chain A: T.713, N.714, F.715, L.919, Q.923, Q.1068, F.1106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.714 NAG-NAG.4: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: A.703, E.1069, N.1071 Chain C: Q.892 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.701 NAG-NAG.6: 5 residues within 4Å: Chain B: K.792, F.797, N.798, S.800, Q.801 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.801 NAG-NAG.7: 4 residues within 4Å: Chain B: N.714, F.715, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: N.1095, G.1096, T.1097, H.1098, F.1100, Y.1107 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: 5 residues within 4Å: Chain C: N.714, F.715, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: A.703, A.710, N.1071 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain B: Y.704, S.705, N.706 Chain C: I.791, Y.793, G.795 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain B: N.120, A.121, N.123, V.125, F.152 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: C.1079, I.1129, N.1131 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: A.703, A.710, E.1069, K.1070, N.1071 Ligand excluded by 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

2024-05-15

Peptides

Spike glycoprotein,Fibritin: ABC
H6 nanobody: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
D

Spike glycoprotein,Fibritin

H6 nanobody