SMTL ID : 7wgv.1

SARS-CoV-2 spike glycoprotein trimer in closed state

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)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.700, L.905 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.784, S.786 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: 8 residues within 4Å: Chain A: T.95, N.221 Chain B: R.444, K.445, S.446, N.447, K.449, E.452 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.445 NAG-NAG.5: 5 residues within 4Å: Chain A: N.109, T.111, N.112, V.114, V.158 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.700, L.905 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: T.95, N.221 Chain C: R.444, K.445, S.446, N.447, K.449, E.452 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: N.109, T.111, N.112, V.114, V.158 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.700, L.905 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain A: R.444, K.445, S.446, N.447, K.449, E.452 Chain C: T.95, N.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.445 NAG-NAG.15: 5 residues within 4Å: Chain C: N.109, T.111, N.112, V.114, V.158 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.603, Q.631, T.632 Chain C: I.817 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.692 Chain C: D.779 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: A.689, E.1055, K.1056, N.1057 Chain C: Q.878 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.1081, H.1084, F.1086 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: N.151, N.152 Chain B: Y.338, A.339, I.455 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.268, N.269 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.330, S.358 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: V.3, N.4, N.124 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: H.133, N.135, N.136, S.138, M.140 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: I.817 Chain B: N.603, Q.631, T.632 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: D.779 Chain B: N.692 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: Q.878 Chain B: A.689, E.1055, K.1056, N.1057 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.1081, H.1084, F.1086 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.151, N.152 Chain C: Y.338, A.339 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.330, S.358 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: V.3, N.4, N.124 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: H.133, N.135, N.136, S.138, M.140 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: I.817 Chain C: N.603, Q.631, T.632 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: D.779 Chain C: N.692 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: Q.878 Chain C: A.689, E.1055, K.1056, N.1057 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.1081, H.1084, F.1086 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain A: Y.338, A.339, I.455 Chain C: N.151, N.152 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.330, S.358 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: V.3, N.4, N.124 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain C: H.133, N.135, N.136, S.138, M.140 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.24: 17 residues within 4Å: Chain A: P.324, F.325, V.328, F.329, I.345, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, I.421, L.500 Chain B: R.395, G.403 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.325, A:V.328, A:F.329, A:I.345, A:Y.352, A:L.355, A:F.361, A:F.364, A:L.374, A:F.379, A:V.382, A:L.500 Salt bridges: B:R.395 EIC.37: 17 residues within 4Å: Chain B: P.324, F.325, V.328, F.329, I.345, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, I.421, L.500 Chain C: R.395, G.403 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.325, B:V.328, B:F.329, B:I.345, B:Y.352, B:L.355, B:F.361, B:F.364, B:L.374, B:F.379, B:V.382, B:L.500 Salt bridges: C:R.395 EIC.50: 16 residues within 4Å: Chain A: R.395 Chain C: P.324, F.325, V.328, F.329, I.345, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, I.421, L.500 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.325, C:V.328, C:F.329, C:I.345, C:Y.352, C:L.355, C:F.361, C:F.364, C:L.374, C:F.379, C:V.382, C:L.500 Salt bridges: A:R.395

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(Non-covalent)

BLR.28: 11 residues within 4Å: Chain A: N.86, I.88, W.91, N.108, V.113, M.164, N.175, R.177, F.179, H.194, L.213 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.91, A:N.108, A:V.113, A:F.179, A:L.213 Hydrogen bonds: A:N.108, A:N.175, A:R.177 Salt bridges: A:R.177, A:H.194 pi-Cation interactions: A:R.177 BLR.41: 11 residues within 4Å: Chain B: N.86, I.88, W.91, N.108, V.113, M.164, N.175, R.177, F.179, H.194, L.213 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.91, B:N.108, B:V.113, B:F.179, B:L.213 Hydrogen bonds: B:N.108, B:N.175, B:R.177 Salt bridges: B:R.177, B:H.194 pi-Cation interactions: B:R.177 BLR.54: 11 residues within 4Å: Chain C: N.86, I.88, W.91, N.108, V.113, M.164, N.175, R.177, F.179, H.194, L.213 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.91, C:N.108, C:V.113, C:F.179, C:L.213 Hydrogen bonds: C:N.108, C:N.175, C:R.177 Salt bridges: C:R.177, 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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