SMTL ID : 7ps6.1

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-44 and Beta-54 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain C: F.20, G.21, N.25 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.20

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 4 residues within 4Å: Chain A: S.31, S.32, N.33, H.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.32, A:H.34

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain C: R.28, F.29, A.30, S.31, N.132, Y.133 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.28, C:S.31 Water bridges: C:S.31, C:S.31, C:N.132, C:N.132 GOL.7: 3 residues within 4Å: Chain D: W.105, D.107 Chain E: Y.51 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Y.51, D:D.107, D:D.107

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

PEG.4: 3 residues within 4Å: Chain D: G.140, T.141, P.191 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.141 PEG.5: 3 residues within 4Å: Chain D: S.193, S.194, T.197 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.193, D:T.197

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

CL.6: 4 residues within 4Å: Chain D: E.46, W.47 Chain E: V.100, F.101 Ligand excluded by PLIP

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

Beta-54 Fab heavy chain: A
Beta-54 Fab light chain: B
Spike protein S1: C
Beta-44 Fab heavy chain: D
Beta-44 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

D
C

E
D

Beta-54 Fab heavy chain

Beta-54 Fab light chain

Spike protein S1

Beta-44 Fab heavy chain

Beta-44 Fab light chain

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