SMTL ID : 7xu1.1

Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-122 Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

13 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: 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.3: 4 residues within 4Å: Chain A: N.788, S.790, Q.791, Q.922 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain B: K.782, N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain C: T.703, N.704, 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.10: 4 residues within 4Å: Chain C: N.788, S.790, Q.791, Q.922 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 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.13: 8 residues within 4Å: Chain C: N.113, A.114, T.115, N.116, V.118, E.145, V.162, P.165 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.116

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

NAG.14: 3 residues within 4Å: Chain A: Y.19, N.52, P.622 Ligand excluded by PLIP NAG.15: 8 residues within 4Å: Chain A: N.113, T.115, N.116, V.118, K.120, F.148, Y.151, V.162 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: N.322, P.570, Q.571, T.572, L.573 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.607, T.609, E.610 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.696, I.1117, G.1118 Chain B: 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: 5 residues within 4Å: Chain A: N.1085, G.1086, 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: 4 residues within 4Å: Chain A: C.6, V.7, N.8, N.128 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: Y.19, F.50, N.52, P.622, T.623 Ligand excluded by PLIP NAG.29: 9 residues within 4Å: Chain B: N.113, T.115, N.116, V.118, K.120, F.148, Y.151, V.162, P.165 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: N.322, P.570, Q.571, T.572, L.573 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.607, T.609, E.610, Q.635 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: N.696, I.1117, G.1118 Chain C: I.781, D.783 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Chain C: Q.882 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: N.1085, G.1086, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: Y.342, A.343, I.459 Chain B: N.155, N.156 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.271, E.272, N.273 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain B: F.329, G.330, N.334, V.358, L.359, N.361, S.362 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: C.6, N.8, N.128 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.322, Q.571, T.572 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: T.298, E.300, N.594 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain A: I.821 Chain C: N.607, T.609, Q.635, R.637 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.696, N.697, I.1117, G.1118 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain A: Q.882 Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: N.1085, G.1086, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.49: 6 residues within 4Å: Chain B: Y.342, A.343, I.459, T.461 Chain C: N.155, N.156 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.271, E.272, N.273 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain C: F.329, G.330, N.334, V.358, L.359, S.362 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.8, N.128 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: Y.19, N.52 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain C: H.137, N.139, N.140, S.142, M.144 Ligand excluded by PLIP

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

BLA.26: 14 residues within 4Å: Chain A: E.87, N.90, I.92, R.93, G.94, W.95, I.110, N.112, V.117, M.168, R.181, F.183, S.196, L.217 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.90, A:R.93, A:W.95, A:I.110, A:V.117, A:F.183, A:L.217, A:L.217 Hydrogen bonds: A:N.112 pi-Cation interactions: A:R.181 BLA.40: 15 residues within 4Å: Chain B: E.87, N.90, I.92, R.93, G.94, W.95, I.110, N.112, V.117, M.168, R.181, F.183, S.196, H.198, L.217 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.90, B:R.93, B:W.95, B:I.110, B:V.117, B:L.217 Hydrogen bonds: B:N.112, B:R.181 pi-Cation interactions: B:R.181, B:H.198 BLA.56: 15 residues within 4Å: Chain C: E.87, N.90, I.92, R.93, G.94, W.95, I.110, N.112, V.117, M.168, R.181, F.183, S.196, H.198, L.217 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.90, C:R.93, C:W.95, C:V.117, C:F.183, C:L.217 Hydrogen bonds: C:N.112 Salt bridges: C:H.198 pi-Cation interactions: C:R.181

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.27: 23 residues within 4Å: Chain A: R.399, 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 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.329, B:V.332, B:I.349, B:A.354, B:Y.356, B:Y.356, B:Y.356, B:L.359, B:Y.360, B:F.365, B:F.368, B:F.383, B:F.383, B:I.425, B:L.504, B:F.506, B:V.515 Salt bridges: A:R.399 EIC.41: 25 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, K.408 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.329, A:F.329, A:I.349, A:L.359, A:F.365, A:F.365, A:F.368, A:L.378, A:L.378, A:F.383, A:F.383, A:I.425, A:F.506 Salt bridges: C:R.399 EIC.52: 28 residues within 4Å: Chain B: R.399, Q.400, T.406, G.407, K.408 Chain C: C.327, P.328, F.329, V.332, F.333, I.349, A.354, Y.356, L.359, Y.360, A.363, S.364, F.365, F.368, L.378, F.383, V.386, A.388, C.423, I.425, L.504, F.506, V.515 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.329, C:Y.356, C:Y.356, C:L.359, C:Y.360, C:F.365, C:F.365, C:F.368, C:F.383, C:F.383, C:I.425, C:L.504, C:F.506, C:V.515 Hydrogen bonds: C:F.365, B:Q.400, B:K.408

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
C

B
B

C
A

Spike glycoprotein