SMTL ID : 7xu3.1

Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: 8 residues within 4Å: Chain A: T.703, N.704, F.705, T.706, L.909, N.912, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.1085, G.1086, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain B: T.703, N.704, F.705, T.706, L.909, N.912, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.909 NAG-NAG.5: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: N.1085, G.1086, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain C: T.703, N.704, F.705, T.706, L.909, N.912, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.8: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.1085, G.1086, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP)

3 x BLA: BILIVERDINE IX ALPHA(Covalent)

BLA.10: 14 residues within 4Å: Chain A: E.87, N.90, R.93, W.95, N.112, A.114, F.166, L.167, R.181, F.183, I.194, S.196, H.198, L.217 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.90, A:N.112, A:A.114, A:F.183, A:L.217 Hydrogen bonds: A:N.112 pi-Cation interactions: A:R.181, A:H.198 BLA.20: 14 residues within 4Å: Chain B: E.87, N.90, R.93, W.95, N.112, A.114, F.166, L.167, R.181, F.183, I.194, S.196, H.198, L.217 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.90, B:N.112, B:A.114, B:F.183, B:L.217 Hydrogen bonds: B:N.112 pi-Cation interactions: B:R.181, B:H.198 BLA.30: 14 residues within 4Å: Chain C: E.87, N.90, R.93, W.95, N.112, A.114, F.166, L.167, R.181, F.183, I.194, S.196, H.198, L.217 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:N.90, C:N.112, C:A.114, C:F.183, C:L.217 Hydrogen bonds: C:N.112 pi-Cation interactions: C:R.181, C:H.198

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

NAG.11: 3 residues within 4Å: Chain A: Y.19, T.20, N.52 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: E.272, N.273 Chain C: K.549 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.322, Q.571 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: G.330, F.333, N.334, L.359 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.696, G.1118 Chain B: I.781, D.783 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Chain B: Q.882 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: V.1120, N.1121 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.19, T.20, N.52 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: K.549 Chain B: E.272, N.273 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: G.330, F.333, N.334, L.359 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.696, G.1118 Chain C: I.781, D.783 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Chain C: Q.882 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: V.1120, N.1121 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Y.19, T.20, N.52 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: K.549 Chain C: E.272, N.273 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.322, Q.571 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: G.330, F.333, N.334, L.359 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: I.781, D.783 Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: Q.882 Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: V.1120, N.1121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qu, K. et al., Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike. Plos Pathog. (2022)

Release Date

2022-07-20

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein

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