SMTL ID : 8yf2.1

Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

4 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: F.20, G.21, F.24, N.25 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.198, S.200, Q.203 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain B: N.304 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.281 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

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

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

NAG.6: 3 residues within 4Å: Chain B: N.35, E.39, W.322 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, C. et al., Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants. Plos Pathog. (2024)

Release Date

2024-10-23

Peptides

Spike protein S1: A
Angiotensin-converting enzyme: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Spike protein S1

Angiotensin-converting enzyme

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