SMTL ID : 8bon.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

13 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: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.704, L.909, N.912, Q.913, Q.1058 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.909, A:N.912 NAG-NAG.5: 4 residues within 4Å: Chain A: T.95, N.221, T.223 Chain C: G.18 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain D: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.909 NAG-NAG.12: 3 residues within 4Å: Chain E: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain E: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain A: E.268, N.269 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: F.329, N.330, S.358, F.361 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: C.2, V.3, N.4, N.124 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: A.693, S.698, N.1061 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain D: N.318 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: F.325, G.326, F.329, N.330 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain D: F.73, N.183, G.219, I.220, N.221, I.222, T.223 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.696, G.1118 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain D: C.2, V.3, N.4, N.124 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: N.267, N.269 Chain E: K.545 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: N.109, T.111, V.114 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: N.267, E.268, N.269 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: N.603, T.605 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: H.642, N.644 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: D.783 Chain E: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: A.693, N.1061 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: T.95, N.221 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: C.2, V.3, N.4, N.124 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.318, Q.567 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thijssen, V. et al., A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-06-28

Peptides

Spike glycoprotein,Fibritin: ADE
Macrocyclic peptide S1B3inL1: BCF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

E
C

B
E

C
D

F
F

Spike glycoprotein,Fibritin

Macrocyclic peptide S1B3inL1

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