SMTL ID : 8jje.1

RBD of SARS-CoV2 spike protein with ACE2 decoy

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: N.53, T.55, E.57, Q.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.57

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.2: 3 residues within 4Å: Chain A: Q.81, Q.101, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.322 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 2 residues within 4Å: Chain A: S.545, N.546 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: G.328, F.331, N.332, L.357 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: F.285, N.432, I.436, W.594 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.594

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: H.374, E.375, H.378, E.402, Y.515 Ligands: SO4.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.375, A:H.378, A:E.402, A:E.402, H2O.1

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 5 residues within 4Å: Chain A: E.375, H.378, E.402, Y.515 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.375 Water bridges: A:Y.515, A:Y.515 Salt bridges: A:H.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urano, E. et al., An inhaled ACE2 decoy confers protection against SARS-CoV-2 infection in preclinical models. Sci Transl Med (2023)

Release Date

2023-12-27

Peptides

Angiotensin-converting enzyme 2: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme 2

Spike glycoprotein