SMTL ID : 7dmu.1 (1 other biounit)

Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 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: 5 residues within 4Å: Chain A: N.36, T.38, E.40, N.41, Q.323 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: Q.64, N.86, H.178 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: K.292, N.305 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: 4 residues within 4Å: Chain A: S.403, D.526, S.528, N.529 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: 3 residues within 4Å: Chain B: F.20, G.21, N.25 No protein-ligand interaction detected (PLIP)

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

NAG.6: 1 residues within 4Å: Chain A: N.415 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.357, E.358, H.361, E.385 Ligands: SO4.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.358, A:H.361, A:E.385, A:E.385, H2O.1

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

SO4.8: 6 residues within 4Å: Chain A: R.256, H.328, E.385, H.488, Y.498 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.498 Salt bridges: A:R.256, A:H.328, A:H.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higuchi, Y. et al., Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme 2

Spike protein S1

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