SMTL ID : 7q9f.1

Beta-50 fab in complex with SARS-CoV-2 beta-Spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-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: 9 residues within 4Å: Chain A: F.339, N.340, A.341, S.368, S.370, R.506 Chain D: Y.50 Chain E: D.103, L.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.370, A:S.370

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: 4 residues within 4Å: Chain A: T.108, N.234 Chain C: K.459, E.462 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.1095, 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: 4 residues within 4Å: Chain A: K.459 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 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: 2 residues within 4Å: Chain C: N.714, Q.923 No protein-ligand interaction detected (PLIP) 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)

2 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.7: 12 residues within 4Å: Chain B: F.339, N.340, A.341, S.368, S.370, L.438, R.506 Chain F: Y.50, T.57 Chain G: W.102, D.103, L.105 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:S.368, B:S.370 Hydrophobic interactions: G:L.105 NAG-NAG-BMA-FUC.13: 10 residues within 4Å: Chain C: F.339, N.340, A.341, S.368, S.370, R.506 Chain H: Y.50, T.57 Chain I: D.103, L.105 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:S.368, C:S.370 Hydrophobic interactions: I:L.105

25 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: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.613 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, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: N.706, G.1128 Chain C: I.791, D.793 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.328, 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-50 light chain: DFH
Beta-50 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-50 light chain

Beta-50 heavy chain

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