SMTL ID : 7s4s.1

Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: F.20, G.21, N.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.25

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

SO4.2: 2 residues within 4Å: Chain A: K.126, N.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.132 Salt bridges: A:K.126 SO4.4: 3 residues within 4Å: Chain B: K.134, S.135, T.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.135 SO4.6: 6 residues within 4Å: Chain C: R.46, G.58, P.60, R.62, F.63, E.82 5 PLIP interactions: 5 interactions with chain C Water bridges: C:Q.38, C:R.46, C:G.58 Salt bridges: C:R.46, C:R.62 SO4.7: 3 residues within 4Å: Chain C: R.18, N.77, R.78 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.18, C:R.18, C:R.78 Salt bridges: C:R.18, C:R.78 SO4.8: 2 residues within 4Å: Chain C: S.158, G.159 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.159 Water bridges: C:Q.157, C:S.161

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

ACT.3: 3 residues within 4Å: Chain A: R.139, K.140, S.141 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:R.31, B:R.31 Hydrogen bonds: A:K.140, A:S.141 Salt bridges: A:R.139, A:K.140 ACT.5: 3 residues within 4Å: Chain B: S.30, R.71, N.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.73 Salt bridges: B:R.71 ACT.9: 3 residues within 4Å: Chain C: S.123, D.124, E.125 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.124, C:E.125 ACT.10: 1 residues within 4Å: Chain C: R.213 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.213 Salt bridges: C:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Front Immunol (2023)

Release Date

2021-09-22

Peptides

Spike protein S1: A
CoV11 heavy chain: B
CoV11 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

CoV11 heavy chain

CoV11 light chain

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