SMTL ID : 7tcq.2 (1 other biounit)

Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-1-1-1-mer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.13, S.118, T.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.119, A:T.119 Salt bridges: A:R.13 SO4.2: 3 residues within 4Å: Chain A: Y.27, T.28, Y.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:Y.32 SO4.3: 3 residues within 4Å: Chain A: R.40, K.63 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.63, A:K.63 Salt bridges: A:R.40, A:K.63 SO4.4: 4 residues within 4Å: Chain A: T.58, Y.60, K.65, K.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58, A:Y.60 Salt bridges: A:K.65, A:K.69 SO4.5: 4 residues within 4Å: Chain A: P.14, N.88, S.115, S.116 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.88, A:S.115, A:S.116 Water bridges: A:S.116, A:S.116 SO4.6: 6 residues within 4Å: Chain A: K.38, K.63, K.67, E.89, D.90 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.90 Water bridges: A:R.40, A:K.67, A:D.90 Salt bridges: A:K.38, A:K.63, A:K.67 SO4.7: 2 residues within 4Å: Chain A: Q.194, S.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.195, A:S.195 Water bridges: A:S.195, A:K.212 SO4.8: 2 residues within 4Å: Chain B: R.187, H.188 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.187, B:H.188 SO4.9: 3 residues within 4Å: Chain A: S.101 Chain B: R.49 Chain C: F.2 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 2 interactions with chain A Water bridges: B:Y.48, C:F.2, C:F.2, C:K.3 Salt bridges: B:R.49 Hydrogen bonds: A:S.101, A:S.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, W. et al., Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability. Structure (2022)

Release Date

2022-08-03

Peptides

Anti-SARS-CoV-2 antibody WS6 Fab heavy chain: A
Anti-SARS-CoV-2 antibody WS6 Fab light chain: B
Pegylated spike S2 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Anti-SARS-CoV-2 antibody WS6 Fab heavy chain

Anti-SARS-CoV-2 antibody WS6 Fab light chain

Pegylated spike S2 peptide

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