SMTL ID : 7ekc.1

Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with human ACE2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 2 residues within 4Å: Chain A: K.8, N.72 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.35, A:E.39, A:N.40 NAG.3: 2 residues within 4Å: Chain A: N.304, M.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.5: 2 residues within 4Å: Chain A: N.414, W.576 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:N.528 NAG.7: 4 residues within 4Å: Chain B: F.20, G.21, F.24, N.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.20, B:F.24 Hydrogen bonds: B:N.25

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, P. et al., Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun (2021)

Release Date

2021-11-03

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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