SMTL ID : 9bnf.1

SARS-CoV-2 spike HexaPro protein in complex with T5A 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)

NAG-NAG.1: 3 residues within 4Å: Chain D: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.717, L.922, 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: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain F: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain F: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

33 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: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: Q.115, N.165 Chain D: R.357, Y.396 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: F.342, N.343 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, G.1131 Chain F: D.796 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1074 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: N.234 Chain D: H.519 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: Y.28, 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: 1 residues within 4Å: Chain D: N.234 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: F.342, N.343, F.374 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.709, N.710 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: A.706, N.1074 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain D: K.113, T.114, Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain F: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain F: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain F: G.232, I.233, N.234 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain F: N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.343, V.367 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.616, T.618 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain F: N.657 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain F: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain F: A.706, N.1074 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain F: N.1134 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: Q.115, N.165, T.167 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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