SMTL ID : 8uum.1

Prototypic SARS-CoV-2 spike (containing K417) in the open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

4 x NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-MAN.1: 1 residues within 4Å: Chain A: N.1134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1134 NAG-MAN.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.801, A:S.803, A:Q.804 NAG-MAN.3: 2 residues within 4Å: Chain B: N.717, L.922 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.717, B:N.717 NAG-MAN.4: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.1098, B:T.1100

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.5: 2 residues within 4Å: Chain A: N.717, L.922 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.717, A:N.717

21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.6: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.1098, T.1100 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain C: N.717 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: S.708, N.709, N.710 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, Q. et al., Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. Elife (2023)

Release Date

2023-11-29

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein

Related Entries With Identical Sequence