SMTL ID : 7tcq.1 (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

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

SO4.1: 3 residues within 4Å: Chain A: Y.27, T.28, Y.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:Y.32 Water bridges: A:R.98 SO4.2: 3 residues within 4Å: Chain A: S.164, G.165 Chain B: K.168 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:D.166, B:D.166, B:D.166, A:V.166 Salt bridges: B:K.168 Hydrogen bonds: A:G.165 SO4.3: 3 residues within 4Å: Chain A: R.13, S.118, T.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.119, A:T.119 Water bridges: A:R.13, A:R.13 Salt bridges: A:R.13 SO4.4: 4 residues within 4Å: Chain A: T.58, Y.60, K.65 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.60 Salt bridges: A:K.65 SO4.5: 1 residues within 4Å: Chain A: E.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1, A:E.1 SO4.6: 6 residues within 4Å: Chain A: T.58, T.59, Y.60, K.65 Chain C: X.12 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.60 Water bridges: A:K.65 Salt bridges: A:K.65 SO4.7: 4 residues within 4Å: Chain A: P.14, N.88, S.115, S.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.88, A:N.88, A:S.116 Water bridges: A:N.88 SO4.8: 4 residues within 4Å: Chain B: S.12, K.106, Y.139, P.140 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.12, B:S.12, B:Y.139 Water bridges: B:K.141 Salt bridges: B:K.106 SO4.9: 4 residues within 4Å: Chain B: E.153, R.154, Q.155, N.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.155, B:N.156, B:N.156 Salt bridges: B:R.154 SO4.10: 8 residues within 4Å: Chain B: R.38, A.79, A.82, L.105, Q.165, D.166, S.167, S.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.79, B:Q.165, B:S.170 Salt bridges: B:R.38 SO4.12: 4 residues within 4Å: Chain C: X.1, F.2, K.3, E.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:R.49 Hydrogen bonds: C:F.2, C:K.3

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 6 residues within 4Å: Chain B: Y.31, Y.33, Y.90, Q.91 Chain C: E.5, Y.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.33 Water bridges: B:Q.91 PEG.13: 3 residues within 4Å: Chain C: X.1, F.2, E.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.5

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
H

B
L

C
C

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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