SMTL ID : 7ps2.1

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-29 and Beta-53 Fabs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 9 residues within 4Å: Chain B: G.21, F.24, N.25, V.49, L.50 Chain D: N.28, V.101, A.102, L.103 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.32, S.33, N.34, N.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.32 GOL.4: 4 residues within 4Å: Chain B: S.57, T.58, G.86, Y.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.57, B:T.58

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

SO4.3: 3 residues within 4Å: Chain A: K.45, Q.48, K.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.48 Salt bridges: A:K.45, A:K.51 SO4.6: 3 residues within 4Å: Chain B: R.37, F.146, R.148 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.37, B:R.148 SO4.7: 4 residues within 4Å: Chain B: F.168 Chain C: S.56, R.58 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.58, C:R.58 SO4.8: 4 residues within 4Å: Chain B: G.158, S.159, T.160, N.169 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.159, B:T.160, B:T.160, B:N.169 SO4.9: 1 residues within 4Å: Chain B: K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Salt bridges: B:K.166 SO4.10: 3 residues within 4Å: Chain B: P.203, A.204, T.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.204, B:T.205 SO4.11: 1 residues within 4Å: Chain B: R.39 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.39 SO4.12: 3 residues within 4Å: Chain C: R.58, Y.60, T.69 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.58 SO4.13: 3 residues within 4Å: Chain C: R.19, K.76, Y.80 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.80, C:Y.80 Salt bridges: C:R.19, C:K.76 SO4.14: 3 residues within 4Å: Chain B: G.184, V.185 Chain C: E.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.1, B:V.185 SO4.15: 2 residues within 4Å: Chain C: R.58 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.58 SO4.16: 1 residues within 4Å: Chain D: S.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.21 SO4.17: 3 residues within 4Å: Chain D: H.105 Chain E: Y.49, T.53 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Salt bridges: D:H.105 Hydrogen bonds: E:T.53, E:T.53 SO4.18: 4 residues within 4Å: Chain B: K.126 Chain E: D.1, S.95, T.96 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:D.1, E:D.1, E:T.96 Salt bridges: B:K.126

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

PEG.5: 3 residues within 4Å: Chain B: R.28, F.29 Chain D: D.55 No protein-ligand interaction detected (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-29 Fab light chain: A
Spike protein S1: B
Beta-29 Fab heavy chain: C
Beta-53 heavy chain: D
Beta-53 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

C
A

D
H

E
L

Beta-29 Fab light chain

Spike protein S1

Beta-29 Fab heavy chain

Beta-53 heavy chain

Beta-53 Fab light chain

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