SMTL ID : 7q9g.1

COVOX-222 fab in complex with SARS-CoV-2 beta-Spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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

NAG-NAG.1: 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.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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:Q.923 NAG-NAG.6: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.277, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: G.336, N.340, L.365, S.368 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: G.336, N.340 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: K.555 Chain C: N.279 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: Q.892 Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: G.336, F.339, N.340, L.365, S.368 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
COVOX-222 heavy chain: DF
COVOX-222 light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
H

F
E

E
L

G
F

Spike glycoprotein

COVOX-222 heavy chain

COVOX-222 light chain

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