SMTL ID : 7y7j.1

SARS-CoV-2 S trimer in complex with 1F Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

hetero-3-1-1-mer

Ligands

15 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: 1 residues within 4Å: Chain A: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: Q.895 Chain C: S.704, A.713, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.704 NAG-NAG.13: 2 residues within 4Å: Chain C: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.717, L.922 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.15: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.122, T.124, V.127, V.171 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.1098, H.1101 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: F.342, N.343 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.122 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.122, T.124, N.125 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: G.339, F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, S. et al., A core epitope targeting antibody of SARS-CoV-2. Protein Cell (2023)

Release Date

2023-02-22

Peptides

Spike glycoprotein: ABC
1F VH: D
1F VL: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
D

Spike glycoprotein

1F VH

1F VL

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