SMTL ID : 7lqw.1

Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex with SARS-CoV-2 S2P spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain C: Y.47, N.80 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain C: S.180 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain C: N.350 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain C: N.362 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain C: E.328, N.622 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain C: N.635 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain C: N.676 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain C: N.728, I.1149 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: E.300, N.301 Chain E: K.577 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain D: Y.47, N.80 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain D: N.301 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain D: N.622 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain D: N.635 Chain E: C.870 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: H.674, N.676 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: N.728, I.1149 Chain E: D.815 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: A.725, N.1093 Ligand excluded by PLIP NAG.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain E: T.489 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain E: N.80 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: K.577 Chain E: N.299, N.301 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain E: N.350 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain E: N.362 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: N.635, T.637, E.638 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain E: N.676 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: D.815 Chain E: N.728 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: A.725, E.1091, N.1093 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe (2021)

Release Date

2021-03-24

Peptides

2-17 Heavy Chain: A
2-17 Light Chain: B
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
B

D
C

E
A

2-17 Heavy Chain

2-17 Light Chain

Spike glycoprotein

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