SMTL ID : 7oan.1

Nanobody C5 bound to Spike

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

15 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: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 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: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 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.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.122, N.125, V.127, F.157 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: F.342, N.343, F.374 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.17, N.137 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.122, N.125, V.127, F.157 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: F.342, N.343, F.374 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: D.796 Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.17, N.137 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.122, N.125, V.127, F.157 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: F.342, N.343, F.374 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.17, N.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19. Nat Commun (2021)

Release Date

2021-08-11

Peptides

Spike glycoprotein: ABC
immunoglobulin mu heavy chain: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
G

F
H

Spike glycoprotein

immunoglobulin mu heavy chain

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