SMTL ID : 7xu4.1

Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 10 residues within 4Å: Chain A: T.99, N.225, T.227 Chain C: R.448, K.449, S.450, N.451, L.452, K.453, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: T.703, N.704, T.706, L.909, N.912, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: K.782, N.788, S.790, Q.791, Q.922 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 10 residues within 4Å: Chain A: R.448, K.449, S.450, N.451, L.452, K.453, E.456 Chain B: T.99, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: T.703, N.704, T.706, L.909, N.912, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: K.782, N.788, S.790, Q.791, Q.922 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 10 residues within 4Å: Chain B: R.448, K.449, S.450, N.451, L.452, K.453, E.456 Chain C: T.99, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain C: T.703, N.704, T.706, L.909, N.912, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: K.782, N.788, S.790, Q.791, Q.922 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.19, N.52, P.622 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain A: N.113, T.115, N.116, V.118, K.120, Y.151, V.162 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.322, Q.571, T.572 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.594 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: N.696, I.1117, G.1118 Chain B: I.781, D.783 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Chain B: Q.882 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: N.155, N.156 Chain C: Y.342, A.343, I.459 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.271, E.272, N.273 Chain C: K.549 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain A: F.329, G.330, N.334, V.358, L.359, S.362 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: C.6, N.8, N.128 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Y.19, N.52, P.622 Ligand excluded by PLIP NAG.29: 7 residues within 4Å: Chain B: N.113, T.115, N.116, V.118, K.120, Y.151, V.162 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.322, Q.571, T.572 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.594 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: N.696, I.1117, G.1118 Chain C: I.781, D.783 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Chain C: Q.882 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: Y.342, A.343, I.459 Chain B: N.155, N.156 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: K.549 Chain B: N.271, E.272, N.273 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: F.329, G.330, N.334, V.358, L.359, S.362 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: C.6, N.8, N.128 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: Y.19, N.52, P.622 Ligand excluded by PLIP NAG.45: 7 residues within 4Å: Chain C: N.113, T.115, N.116, V.118, K.120, Y.151, V.162 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.322, Q.571, T.572 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.594 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.607, T.609, Q.635 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain A: I.781, D.783 Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain A: Q.882 Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain B: Y.342, A.343, I.459 Chain C: N.155, N.156 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: K.549 Chain C: N.271, E.272, N.273 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain C: F.329, G.330, N.334, V.358, L.359, S.362 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: C.6, N.8, N.128 Ligand excluded by PLIP

3 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.26: 16 residues within 4Å: Chain A: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, M.168, N.179, R.181, F.183, S.196, H.198, L.217 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.90, A:W.95, A:I.110, A:V.117, A:F.183, A:L.217 Hydrogen bonds: A:N.112, A:N.179, A:R.181 Salt bridges: A:H.198 pi-Cation interactions: A:R.181, A:H.198 BLA.41: 16 residues within 4Å: Chain B: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, M.168, N.179, R.181, F.183, S.196, H.198, L.217 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.90, B:W.95, B:I.110, B:V.117, B:F.183, B:L.217 Hydrogen bonds: B:N.112, B:N.179, B:R.181 Salt bridges: B:H.198 pi-Cation interactions: B:R.181, B:H.198 BLA.57: 16 residues within 4Å: Chain C: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, M.168, N.179, R.181, F.183, S.196, H.198, L.217 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:N.90, C:W.95, C:I.110, C:V.117, C:F.183, C:L.217 Hydrogen bonds: C:N.112, C:N.179, C:R.181 Salt bridges: C:H.198 pi-Cation interactions: C:R.181, C:H.198

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.27: 24 residues within 4Å: Chain A: R.399, Q.400, T.406, G.407 Chain B: C.327, P.328, F.329, V.332, F.333, I.349, A.354, Y.356, L.359, Y.360, F.365, F.368, L.378, F.383, V.386, A.388, I.425, L.504, F.506, V.515 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.329, B:V.332, B:I.349, B:I.349, B:A.354, B:Y.356, B:L.359, B:Y.360, B:F.365, B:F.368, B:F.368, B:F.383, B:V.386, B:L.504, B:F.506 Salt bridges: A:R.399 EIC.42: 24 residues within 4Å: Chain B: R.399, Q.400, T.406, G.407 Chain C: C.327, P.328, F.329, V.332, F.333, I.349, A.354, Y.356, L.359, Y.360, F.365, F.368, L.378, F.383, V.386, A.388, I.425, L.504, F.506, V.515 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.329, C:V.332, C:I.349, C:I.349, C:A.354, C:Y.356, C:Y.360, C:F.365, C:F.368, C:F.368, C:F.383, C:V.386, C:L.504, C:F.506 Salt bridges: B:R.399 EIC.43: 24 residues within 4Å: Chain A: C.327, P.328, F.329, V.332, F.333, I.349, A.354, Y.356, L.359, Y.360, F.365, F.368, L.378, F.383, V.386, A.388, I.425, L.504, F.506, V.515 Chain C: R.399, Q.400, T.406, G.407 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.329, A:V.332, A:I.349, A:I.349, A:A.354, A:Y.356, A:L.359, A:Y.360, A:F.365, A:F.368, A:F.368, A:F.383, A:V.386, A:L.504, A:F.506 Salt bridges: C:R.399

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
A

B
C

C
B

Spike glycoprotein

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