SMTL ID : 8vkp.1

Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and 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: 4 residues within 4Å: Chain B: Q.64, Q.84, N.86, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: S.403, S.528, N.529 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: H.10, N.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.10 NAG.4: 3 residues within 4Å: Chain B: N.36, E.40, Q.323 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.36, B:T.38, B:E.40, B:Q.323, B:Q.323 NAG.5: 3 residues within 4Å: Chain B: K.9, N.73, T.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.75 NAG.6: 1 residues within 4Å: Chain B: N.305 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.305 NAG.7: 2 residues within 4Å: Chain B: N.415, W.577 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein. Nat Commun (2024)

Release Date

2024-02-14

Peptides

Spike protein S1: A
Processed angiotensin-converting enzyme 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike protein S1

Processed angiotensin-converting enzyme 2

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