SMTL ID : 8h3d.1

Structure of apo SARS-CoV-2 spike protein with one RBD up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: A.27, Y.28, N.61, T.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.28, A:T.63 NAG.2: 2 residues within 4Å: Chain A: N.603, T.604 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.657 NAG.4: 2 residues within 4Å: Chain B: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.343 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.603, T.604 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.603, B:T.604 NAG.8: 1 residues within 4Å: Chain B: N.657 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain C: Y.28, N.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.28 NAG.10: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: G.339, N.343, L.368 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.339 NAG.12: 2 residues within 4Å: Chain C: E.309, N.603 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.657 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. Acs Cent.Sci. (2023)

Release Date

2023-03-22

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin

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