SMTL ID : 7wgy.1

SARS-CoV-2 spike glycoprotein trimer in Intermediate state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

8 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: 1 residues within 4Å: Chain A: N.700 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.109, V.114, V.158 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.158 NAG-NAG.5: 3 residues within 4Å: Chain B: N.700, L.905, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.700 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.784, S.786 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.692, G.1114 Chain B: D.779 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: E.1055, N.1057 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.1081, T.1083, H.1084 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.267, E.268, N.269 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.330 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.692 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: E.1055, N.1057 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.1081, T.1083, H.1084 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1117 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.267, N.269 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.692, G.1114 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.1081, T.1083, H.1084 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.1117 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: F.325, G.326, E.327, N.330 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, M.M. et al., Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies. Cell Discov (2022)

Release Date

2023-01-04

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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