SMTL ID : 8hec.1

SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 2 conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

17 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: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 NAG-NAG.8: 1 residues within 4Å: Chain B: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.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.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.18: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.165, C.166, T.167 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: S.112, N.164, N.165 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.1072, N.1074 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.165, T.167 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chu, X. et al., Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2. Biochem.Biophys.Res.Commun. (2023)

Release Date

2023-04-26

Peptides

Spike glycoprotein: ABC
rabbit antibody 9H1 light chain: DFH
rabbit antibody 9H1 heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

Spike glycoprotein

rabbit antibody 9H1 light chain

rabbit antibody 9H1 heavy chain

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