SMTL ID : 7my3.1

CryoEM structure of neutralizing nanobody Nb12 in complex with SARS-CoV2 spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: G.339, F.342, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain B: N.717, L.922 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.343, S.371, S.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.371 NAG-NAG.8: 2 residues within 4Å: Chain B: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.17: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.19: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature (2021)

Release Date

2021-06-16

Peptides

Spike glycoprotein: ABC
Nanobody Nb12: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
H

E
E

F
D

Spike glycoprotein

Nanobody Nb12

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