SMTL ID : 7wgx.1

SARS-CoV-2 spike glycoprotein trimer in closed state after treatment with Cathepsin L

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: 4 residues within 4Å: Chain A: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain A: T.95, N.221, T.223 Chain C: R.444, K.445, S.446, N.447, K.449, E.452 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.445 NAG-NAG.4: 4 residues within 4Å: Chain A: N.109, T.111, 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 A: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 9 residues within 4Å: Chain A: R.444, K.445, S.446, N.447, K.449, E.452 Chain B: T.95, N.221, T.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.445 NAG-NAG.9: 4 residues within 4Å: Chain B: N.109, T.111, V.114, V.158 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.158 NAG-NAG.10: 3 residues within 4Å: Chain B: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 9 residues within 4Å: Chain B: R.444, K.445, S.446, N.447, K.449, E.452 Chain C: T.95, N.221, T.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.445 NAG-NAG.14: 4 residues within 4Å: Chain C: N.109, T.111, V.114, V.158 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.158 NAG-NAG.15: 3 residues within 4Å: Chain C: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP)

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

NAG.16: 5 residues within 4Å: Chain A: F.325, G.326, N.330, L.355, S.358 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.603, Q.631 Chain B: I.817 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.1117 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.268, N.269 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.692, G.1114 Chain B: D.779 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.152 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: F.325, G.326, N.330, L.355, S.358 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.603, Q.631 Chain C: I.817 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1117 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.692, G.1114 Chain C: D.779 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: F.325, G.326, N.330, L.355, S.358 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: I.817 Chain C: N.603, Q.631 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.1117 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: D.779 Chain C: N.692, G.1114 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.152 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 Ligand excluded by PLIP

3 x BLR: 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid(Covalent)

BLR.25: 10 residues within 4Å: Chain A: N.86, I.88, W.91, I.106, N.108, V.113, R.177, F.179, H.194, L.213 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.86, A:W.91, A:I.106, A:N.108, A:V.113, A:L.213 Salt bridges: A:H.194 pi-Cation interactions: A:R.177 BLR.35: 10 residues within 4Å: Chain B: N.86, I.88, W.91, I.106, N.108, V.113, R.177, F.179, H.194, L.213 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.86, B:W.91, B:I.106, B:N.108, B:V.113, B:L.213 Salt bridges: B:H.194 pi-Cation interactions: B:R.177 BLR.45: 10 residues within 4Å: Chain C: N.86, I.88, W.91, I.106, N.108, V.113, R.177, F.179, H.194, L.213 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:N.86, C:W.91, C:I.106, C:N.108, C:V.113, C:L.213 Salt bridges: C:H.194 pi-Cation interactions: C:R.177

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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