SMTL ID : 8p99.1

SARS-CoV-2 S-protein:D614G mutant in 1-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.720, L.925 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: G.345, N.349 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.170, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.720 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.337, I.338, Q.586 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: H.1086, D.1087, G.1088, N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.349, N.376, S.377 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.377 NAG-NAG.8: 3 residues within 4Å: Chain C: N.720, L.925, Q.929 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: E.287, N.288 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: G.345, N.349 No protein-ligand interaction detected (PLIP)

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

NAG.11: 1 residues within 4Å: Chain A: N.1137 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.712 Chain B: D.799 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.804, S.806 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Y.34, N.67 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: A.709, N.1077 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.1101, F.1106 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.288 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.471 Chain B: N.240, T.242 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.622, T.624 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.712, I.1133, G.1134 Chain C: D.799 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.1101, H.1104, F.1106 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.170 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.288 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.663 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.804 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.1077 Chain C: Q.898 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: T.114, N.240, T.242 Chain C: E.471 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1137 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.1101, H.1104, F.1106 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: A.709, E.1075, N.1077 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.712 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.804, S.806 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.622, T.624 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gargantilla, M. et al., C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein. J.Med.Chem. (2023)

Release Date

2023-09-27

Peptides

Spike protein S1,Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1,Spike glycoprotein

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