SMTL ID : 7lqv.1

Cryo-EM structure of NTD-directed neutralizing antibody 4-8 Fab in complex with SARS-CoV-2 S2P spike

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: Y.47, F.78, N.80, P.650 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain A: N.141, E.173, S.174, F.176 Chain D: I.106 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.301 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: P.349, N.350, Q.599 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.362, S.392 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.622, T.623 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.635, T.637, Q.663 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.676 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.728, G.1150 Chain B: D.815 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: A.725, N.1093 Chain B: Q.914 Ligand excluded by PLIP NAG.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: Y.47, N.49, N.80 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: K.577 Chain B: N.301 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.350, Q.599 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.635 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.676 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.728, G.1150 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: A.725, N.1093 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.184 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: Y.47, N.80 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: K.577 Chain C: N.301 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.350, Q.599 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: F.357, N.362, S.392, F.393 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.635 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.676 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: D.815 Chain C: N.728 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: A.725, 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

Spike glycoprotein: ABC
4-8 Heavy Chain: DFH
4-8 Light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
W

H
Y

E
L

G
X

I
Z

Spike glycoprotein

4-8 Heavy Chain

4-8 Light chain

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