SMTL ID : 8xv1.1

Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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: 4 residues within 4Å: Chain B: S.402, D.525, 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.2: 2 residues within 4Å: Chain B: 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.3: 10 residues within 4Å: Chain B: N.85, T.329, A.330, E.357, H.360, H.383, E.384, F.486, Y.492, R.496 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.496, B:Y.492

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

NAG.4: 2 residues within 4Å: Chain A: H.325, N.329 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.325 NAG.5: 3 residues within 4Å: Chain A: R.332, N.340, T.342 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.304 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain B: N.414 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain B: N.35, E.39, Q.322 No protein-ligand interaction detected (PLIP)

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

Related Entries With Identical Sequence