SMTL ID : 7q6e.1

Beta049 fab in complex with SARS-CoV2 beta-Spike glycoprotein, The Beta mAb response underscores the antigenic distance to other SARS-CoV-2 variants

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-FUC.1: 16 residues within 4Å: Chain A: F.339, N.340, A.341, V.364, S.368, A.369, S.370, R.506 Chain C: Y.498, Y.502 Chain D: Y.50, T.57 Chain E: S.100, A.103, I.105, F.107 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: A:S.368, D:T.57 Hydrophobic interactions: E:A.103, E:I.105, E:F.107 NAG-NAG-BMA-MAN-MAN-MAN-FUC.13: 12 residues within 4Å: Chain B: Y.502 Chain C: F.339, N.340, A.341, S.368, R.506 Chain H: Y.50, T.57 Chain I: S.100, A.103, I.105, F.107 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain I, 1 interactions with chain H Hydrogen bonds: C:S.368, H:T.57 Hydrophobic interactions: I:A.103, I:I.105, I:F.107

14 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: S.456, K.459 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.4: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.10: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.15: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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-MAN-MAN-FUC.7: 15 residues within 4Å: Chain A: Y.502 Chain B: N.340, A.341, V.364, S.368, A.369, L.438, R.506 Chain F: Y.50, T.57 Chain G: V.2, T.28, A.103, I.105, F.107 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: G:V.2, G:T.28, G:F.107, G:I.105, G:F.107 Hydrogen bonds: B:S.368, F:T.57

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

NAG.18: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.348 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.706, I.1127, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.328, T.330, Q.577 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

Spike glycoprotein: ABC
Beta-49 light chain: DFH
Beta-49 heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

F
F

H
K

E
H

G
E

I
J

Spike glycoprotein

Beta-49 light chain

Beta-49 heavy chain

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