SMTL ID : 7v85.1

Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

31 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 A: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.331, I.332, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.709, I.1130 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.10: 2 residues within 4Å: Chain A: N.1098, D.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: Q.115, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.24: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain C: N.1098, T.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.32: 4 residues within 4Å: Chain A: Y.28, N.30, F.59, N.61 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.61 NAG.33: 2 residues within 4Å: Chain A: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain A: N.603 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.603 NAG.35: 2 residues within 4Å: Chain A: H.655, N.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.655 NAG.36: 2 residues within 4Å: Chain B: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.37: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.123 Hydrogen bonds: B:N.122, B:T.124 NAG.38: 2 residues within 4Å: Chain B: N.603, T.604 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Chain B: H.655, N.657 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.655 NAG.40: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 No protein-ligand interaction detected (PLIP) NAG.41: 2 residues within 4Å: Chain C: N.165, T.167 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.165 NAG.42: 3 residues within 4Å: Chain C: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP) NAG.43: 2 residues within 4Å: Chain C: N.603, T.604 No protein-ligand interaction detected (PLIP) NAG.44: 1 residues within 4Å: Chain C: N.657 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.657

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2,Green fluorescent protein: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
H

Spike glycoprotein

Angiotensin-converting enzyme 2,Green fluorescent protein

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