SMTL ID : 9kud.1 (1 other biounit)

Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, R.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.40, A:N.40 NAG.2: 4 residues within 4Å: Chain A: K.8, N.72, T.74, L.75 No protein-ligand interaction detected (PLIP) NAG.3: 5 residues within 4Å: Chain A: K.398, S.402, D.525, S.527, N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.402 NAG.5: 7 residues within 4Å: Chain B: V.10, A.13, R.15, F.16, A.17, N.23, S.68 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.13 Hydrogen bonds: B:R.15, B:A.17, B:N.23 NAG.6: 1 residues within 4Å: Chain B: N.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.12

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX. Structure (2025)

Release Date

2025-08-06

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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