SMTL ID : 7zce.1

SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-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: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: K.310, P.600, G.601, N.603, T.604 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: G.339, E.340, N.343 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: D.796 Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.603 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.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.122, T.124, F.157 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: G.339, E.340, N.343 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: D.796 Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.122 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: G.339, E.340, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milazzo, F.M. et al., Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery. Mol.Ther. (2022)

Release Date

2022-10-12

Peptides

Spike glycoprotein,Fibritin: ABC
scFv76 single chain fragment: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

Spike glycoprotein,Fibritin

scFv76 single chain fragment

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