SMTL ID : 7vq0.1

Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

17 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain A: V.120, N.121, N.122, N.125, V.126, V.127, K.129, E.154, F.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.125, A:K.129 NAG-NAG.3: 2 residues within 4Å: Chain A: N.165 Chain F: D.53 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.616, T.618 Chain B: I.834, Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.616, T.618, Q.644 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain C: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain A: I.850 Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.23: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.8: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1074 NAG-NAG-FUC.24: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1074

6 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.27: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: Y.144 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: G.339, N.343 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: T.307, N.603 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.39: 10 residues within 4Å: Chain B: Q.115, V.130, E.132, N.165, C.166, T.167 Chain D: T.28, D.98, N.100, Y.105 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.343, F.374 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: F.157, Y.160 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: K.147, N.148, N.149 Ligand excluded by PLIP NAG.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: T.108, T.236 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: N.343, V.367, S.373, F.374 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: E.309, N.603 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maeda, R. et al., A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron. Commun Biol (2022)

Release Date

2022-07-20

Peptides

Spike glycoprotein: ABC
Neutralizing nanobody P86: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Neutralizing nanobody P86