SMTL ID : 8uul.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.343, V.367, S.371, F.374 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.717, Q.926 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.343, S.371, S.373, F.374 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.616 Chain C: I.834 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: T.108, T.236 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.1098 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: I.834 Chain C: N.616 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1074 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
A

B
B

C
C

Spike glycoprotein

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