SMTL ID : 8dlr.1

Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.28 NAG.2: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.122, A:T.124, A:N.125 NAG.3: 3 residues within 4Å: Chain A: N.149, S.151, W.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 NAG.4: 3 residues within 4Å: Chain A: E.132, N.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.164 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: 1 residues within 4Å: Chain A: 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 4-8 heavy chain: B
Fab 4-8 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

Fab 4-8 heavy chain

Fab 4-8 light chain

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