SMTL ID : 8jyp.1

Structure of SARS-CoV-2 XBB.1.5 spike RBD in complex with ACE2

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: 3 residues within 4Å: Chain A: T.410 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, H.327, P.328, T.329, A.330, E.357, H.360, E.384, F.486, Y.492 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.492

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

NAG.4: 1 residues within 4Å: Chain A: N.338 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.304 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.414 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.414 NAG.7: 3 residues within 4Å: Chain B: N.35, E.39, Q.322 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.39, B:Q.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB.1.5 variant. To Be Published

Release Date

2024-01-03

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

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