SMTL ID : 8dls.1

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 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: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: N.149, M.153 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.165 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.234 NAG.6: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Spike glycoprotein: A
Fab 4A8 heavy chain: B
Fab 4A8 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

Fab 4A8 heavy chain

Fab 4A8 light chain

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