SMTL ID : 8iov.1

Structure of SARS-CoV-2 XBB.1 spike RBD in complex with ACE2

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: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: K.398, S.402, D.525, 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: 10 residues within 4Å: Chain A: N.85, H.327, T.329, A.330, E.357, H.360, H.383, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.492

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

NAG.5: 1 residues within 4Å: Chain A: N.304 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414 NAG.7: 2 residues within 4Å: Chain B: N.338, T.340 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.340 Hydrogen bonds: B:N.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun (2023)

Release Date

2023-05-24

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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