SMTL ID : 7upy.1

An antibody from single human VH-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-3-3-3-mer

Ligands

16 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: 3 residues within 4Å: Chain A: C.15, V.16, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.717, T.719, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.616, T.618 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 9 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.458 NAG-NAG.26: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain A: I.834, Q.836 Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.29: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 5 residues within 4Å: Chain A: E.132, N.165 Chain C: Y.351, I.468 Chain F: S.55 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 6 residues within 4Å: Chain B: N.122, T.124, N.125, E.154, E.169, V.171 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.169, B:V.171 NAG-NAG-MAN.19: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 3 residues within 4Å: Chain C: N.122, T.124, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.31: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.34: 5 residues within 4Å: Chain B: Y.351, I.468 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP)

6 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.7: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 4 residues within 4Å: Chain A: N.343, V.367 Chain H: Y.103 Chain I: T.56 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.103 NAG-NAG-FUC.18: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.21: 6 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Chain D: Y.103 Chain E: T.56 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.30: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.33: 6 residues within 4Å: Chain C: F.338, G.339, N.343, V.367 Chain F: Y.103 Chain G: T.56 No protein-ligand interaction detected (PLIP)

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

NAG.35: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: K.147, N.149 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: K.462 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: K.147, N.149 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: K.147, N.149, M.153 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: Y.1155, N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, S. et al., An antibody from single human V H -rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Sci Immunol (2022)

Release Date

2022-08-10

Peptides

Spike glycoprotein: ABC
SP1-77 Fab heavy chain: DFH
SP1-77 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
F

E
L

G
E

I
G

Spike glycoprotein

SP1-77 Fab heavy chain

SP1-77 Fab light chain

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