SMTL ID : 7v87.1

Local refinement of SARS-CoV-2 S-Kappa variant (B.1.617.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 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.1: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain B: S.420, N.546 No protein-ligand interaction detected (PLIP)

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.2: 1 residues within 4Å: Chain B: N.90 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain B: N.53, Q.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.53, B:E.57, B:Q.340 NAG.5: 2 residues within 4Å: Chain B: Q.101, N.103 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.322 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: D.431, N.432, E.433 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Local refinement of SARS-CoV-2 S-Kappa variant (B.1.617.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: A
Angiotensin-converting enzyme 2,Angiotensin-converting enzyme 2 (ACE2) ectodomain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Spike glycoprotein

Angiotensin-converting enzyme 2,Angiotensin-converting enzyme 2 (ACE2) ectodomain

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