SMTL ID : 8ka8.1

Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: F.10, N.11 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.356, H.360, E.384 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.356, A:H.356, A:H.360, A:E.384, A:E.384

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

NAG.4: 3 residues within 4Å: Chain A: N.35, E.39, R.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.39, A:E.39 NAG.5: 3 residues within 4Å: Chain A: K.60, K.63, N.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.60, A:K.63 Hydrogen bonds: A:N.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, S. et al., Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs. J.Virol. (2024)

Release Date

2024-01-31

Peptides

Angiotensin-converting enzyme: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Angiotensin-converting enzyme

Spike protein S1

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