SMTL ID : 9aru.1

COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain G: R.457, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.3: 4 residues within 4Å: Chain A: D.796, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: D.1127, N.1134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.1127 NAG-NAG.6: 4 residues within 4Å: Chain A: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.7: 8 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain D: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.922, D:N.925 NAG-NAG.9: 4 residues within 4Å: Chain D: D.796, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain D: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain D: D.1127, N.1134 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.1127 NAG-NAG.12: 4 residues within 4Å: Chain D: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.706 NAG-NAG.13: 8 residues within 4Å: Chain D: R.457, S.459, N.460, K.462, E.465 Chain G: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain G: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.922, G:N.925 NAG-NAG.15: 4 residues within 4Å: Chain G: D.796, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain G: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain G: D.1127, N.1134 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.1127 NAG-NAG.18: 4 residues within 4Å: Chain G: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:A.706

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

NAG.19: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: E.132, N.165 Chain G: I.468 Chain H: Y.108 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: N.616, T.618, E.619, Q.644, T.645 Chain D: I.834 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: C.15, N.17 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: I.468 Chain B: Y.108 Chain D: E.132, N.165 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain D: N.616, T.618, E.619, Q.644, T.645 Chain G: I.834 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain D: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: C.15, N.17 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain D: I.468 Chain E: Y.108 Chain G: E.132, N.165 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain A: I.834 Chain G: N.616, T.618, E.619, Q.644, T.645 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain G: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.331, Q.580 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: C.15, N.17 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: Y.28, T.29, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Taeye, S.W. et al., Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy. Plant Biotechnol J (2025)

Release Date

2025-01-29

Peptides

Spike glycoprotein: ADG
COVA2-15 heavy chain variable region: BEH
COVA2-15 kappa chain variable region: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
D

H
E

C
L

F
F

I
G

Spike glycoprotein

COVA2-15 heavy chain variable region

COVA2-15 kappa chain variable region

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