SMTL ID : 7zbu.1

CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: G.370, N.374 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: N.362, Q.611 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.611 NAG.3: 3 residues within 4Å: Chain A: C.46, N.48, N.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 NAG.4: 6 residues within 4Å: Chain A: N.153, T.155, N.156, V.158, K.160, V.202 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.155 Hydrogen bonds: A:T.155, A:K.160, A:K.160 NAG.5: 1 residues within 4Å: Chain A: N.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.196 NAG.6: 3 residues within 4Å: Chain A: N.311, E.312, N.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.312 NAG.7: 2 residues within 4Å: Chain A: F.90, N.92 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: H.177, N.180, S.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:S.182, A:S.182

1 x 3Q9: 3-[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid(Non-covalent)

3Q9.9: 12 residues within 4Å: Chain A: N.130, I.132, R.133, G.134, W.135, N.152, V.157, M.208, R.221, F.223, H.238, L.257 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.135, A:N.152, A:F.223, A:L.257, A:L.257 Hydrogen bonds: A:N.152, A:R.221, A:R.221 Salt bridges: A:R.221, A:H.238 pi-Cation interactions: A:R.221, A:H.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seow, J. et al., A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination. Cell Rep (2022)

Release Date

2022-08-17

Peptides

Spike glycoprotein: A
P008_60 antibody, Heavy chain: B
P008_60 antibody, Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

P008_60 antibody, Heavy chain

P008_60 antibody, Light chain

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