SMTL ID : 9iu1.1

Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)

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: N.35, T.37, E.39, Q.322 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: S.402, S.527, N.528 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.3: 2 residues within 4Å: Chain A: K.8, N.72 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: 11 residues within 4Å: Chain A: Q.84, N.85, H.327, T.329, A.330, E.357, L.373, H.383, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.327

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

NAG.5: 2 residues within 4Å: Chain A: P.303, N.304 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: N.329, L.427 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yajima, H. et al., Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nat Commun (2024)

Release Date

2024-10-09

Peptides

Processed angiotensin-converting enzyme 2: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Processed angiotensin-converting enzyme 2

Spike glycoprotein

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