SMTL ID : 7ps1.1

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-27 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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 Hydrogen bonds: A:N.25

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.28, F.29, A.30, S.31, N.132, Y.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.31, A:S.31 GOL.3: 5 residues within 4Å: Chain A: S.57, T.58, G.86, V.89, Y.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.58, A:T.58 GOL.6: 3 residues within 4Å: Chain A: G.167 Chain B: Y.102 Chain C: Y.50 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:D.105 Hydrogen bonds: C:Y.50 GOL.7: 4 residues within 4Å: Chain B: R.19, S.70, R.71, Y.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.19, B:S.70

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: T.112 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.166, F.172 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: S.124, V.125 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: N.210, R.211, G.212, E.213 Ligand excluded by PLIP

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 1 residues within 4Å: Chain B: G.26 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: H.168 Chain C: D.167 Ligand excluded by PLIP IOD.11: 6 residues within 4Å: Chain B: P.171, S.181, L.182, S.183 Chain C: S.162, S.176 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain C: G.42 Ligand excluded by PLIP

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

PEG.12: 6 residues within 4Å: Chain B: G.42, K.43 Chain C: G.9, Y.88, G.100, G.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.42 Water bridges: B:Q.39 PEG.13: 7 residues within 4Å: Chain A: N.99, Y.135 Chain C: S.30, S.32, S.33, Y.92, G.93 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.30, C:S.32 Water bridges: A:E.88, A:E.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe (2022)

Release Date

2021-12-15

Peptides

Spike protein S1: A
Beta-27 Fab heavy chain: B
Beta-27 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
B

Spike protein S1

Beta-27 Fab heavy chain

Beta-27 Fab light chain

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