SMTL ID : 7rbu.1

SARS-CoV-2 Spike in complex with PVI.V6-14 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 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: 4 residues within 4Å: Chain A: N.109, T.111, V.114, V.158 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.158 NAG-NAG.2: 3 residues within 4Å: Chain A: C.2, N.4, N.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.124

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

NAG.3: 3 residues within 4Å: Chain A: T.95, N.221, T.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.95 NAG.4: 2 residues within 4Å: Chain A: Y.15, N.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 NAG.5: 1 residues within 4Å: Chain A: N.136 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Altomare, C.G. et al., Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain. Mbio (2022)

Release Date

2022-05-04

Peptides

Spike protein S1: A
PVI.V6-14 Fab heavy chain, variable region: B
PVI.V6-14 Fab light chain, variable region: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
H

C
L

Spike protein S1

PVI.V6-14 Fab heavy chain, variable region

PVI.V6-14 Fab light chain, variable region

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