SMTL ID : 7sjs.1

Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: K.144, D.145, V.170, Q.172, S.178 Chain B: Y.179, S.181 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.144 Hydrogen bonds: A:S.178, A:S.178 Water bridges: A:K.144, A:Q.172, A:Q.172, B:S.181

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

SO4.2: 2 residues within 4Å: Chain A: T.194, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.194 Salt bridges: A:R.211 SO4.3: 4 residues within 4Å: Chain A: T.108, T.109, P.150, K.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.108, A:T.109, A:T.109 Salt bridges: A:K.202 SO4.5: 4 residues within 4Å: Chain A: E.1, V.2 Chain C: H.20, T.21 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.21, C:T.21 Salt bridges: C:H.20 Water bridges: A:V.2, A:V.2, A:G.26 SO4.6: 5 residues within 4Å: Chain A: F.27, T.28, Y.32 Chain C: N.19, H.20 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:H.20 Hydrogen bonds: A:T.28, A:T.28, A:Y.32 SO4.7: 2 residues within 4Å: Chain B: R.30 Chain C: E.5 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.5 Water bridges: C:D.7, B:R.30 Salt bridges: B:K.29, B:R.30

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: Y.2, D.91, S.92, S.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.92, B:S.93, B:S.93 Water bridges: B:H.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, P. et al., A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection. Sci Transl Med (2022)

Release Date

2022-01-12

Peptides

CC40.8 Fab heavy chain: A
CC40.8 Fab light chain: B
stem helix peptide of Spike protein S2': C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

CC40.8 Fab heavy chain

CC40.8 Fab light chain

stem helix peptide of Spike protein S2'

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