SMTL ID : 9bng.1

SARS-CoV-2 spike HexaPro protein in complex with T18A trimeric antagonist

Coordinates

PDB Format Compare

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)(Non-covalent)

NAG-NAG.1: 6 residues within 4Å: Chain B: P.330, N.331, T.333, P.579, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain D: E.281, N.282 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.282 NAG-NAG.5: 2 residues within 4Å: Chain D: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain F: T.114, Q.115, E.132, N.165, T.167 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.114, F:T.114 NAG-NAG.9: 3 residues within 4Å: Chain F: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain F: G.339, F.342, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain F: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.804

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

NAG.13: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: Q.115, N.165 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: S.591, N.616, T.618, E.619 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: S.708, N.709, N.710 Chain F: D.796 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: F.342, N.343 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain D: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: G.232, N.234 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: F.342, N.343 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: D.796 Chain D: N.709, N.710 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.1074 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: G.232, I.233, N.234 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: K.558 Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain F: N.657 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain D: D.796 Chain F: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: Q.895 Chain F: N.1074 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain F: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Young, T. et al., Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist. To Be Published

Release Date

2025-08-27

Peptides

Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2: ACE
Spike glycoprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2

Spike glycoprotein

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