SMTL ID : 7prz.1

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-22 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 3 residues within 4Å: Chain B: G.21, F.24, N.25 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.2: 7 residues within 4Å: Chain C: N.35, K.36, T.37, W.56, A.57, S.58, G.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.35, C:T.37, C:T.37, C:S.58, C:S.58, C:N.35

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

SO4.3: 3 residues within 4Å: Chain A: G.117, T.118, T.119 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: S.7, G.8 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain B: K.60 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: S.57, N.119, Y.190 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: D.87, Y.190 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: G.158, S.159, T.160, N.169 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: R.28, F.29 Ligand excluded by PLIP SO4.10: 1 residues within 4Å: Chain B: Y.78 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: Y.109 Chain B: R.85, E.88, Q.91, N.99 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: R.90 Chain C: R.60, S.62, G.63 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: A.1, Q.27, S.99 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain C: Q.48, K.51 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: Q.39 Chain C: Q.44, K.45, P.46, G.47, Q.48 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: P.65, D.66 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain C: R.114 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-22 Fab heavy chain: A
Spike protein S1: B
Beta-22 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
E

C
L

Beta-22 Fab heavy chain

Spike protein S1

Beta-22 Fab light chain

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