SMTL ID : 7xu6.1

Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, 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: 11 residues within 4Å: Chain A: T.99, T.100, 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, F.705, T.706, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: K.782, N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 11 residues within 4Å: Chain A: R.448, K.449, S.450, N.451, L.452, K.453, E.456 Chain B: T.99, T.100, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: T.703, N.704, F.705, T.706, L.909, 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: 2 residues within 4Å: Chain B: V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 11 residues within 4Å: Chain B: R.448, K.449, S.450, N.451, L.452, K.453, E.456 Chain C: T.99, T.100, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain C: T.703, N.704, F.705, T.706, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: K.782, N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: 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: 9 residues within 4Å: Chain A: N.113, T.115, N.116, V.118, K.120, F.148, Y.151, V.162, P.165 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.322, Q.571 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.594 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: N.607, T.609, E.610, Q.635 Chain B: Q.823 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, N.697, 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: 4 residues within 4Å: Chain A: N.155, N.156 Chain C: Y.342, I.459 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: N.271, E.272, N.273, T.277 Chain C: K.549 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain A: F.329, G.330, N.334, L.359, N.361, S.362 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.8, T.10, N.128, D.129 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.19, N.52, P.622 Ligand excluded by PLIP NAG.28: 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.29: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.594, T.595 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.607, T.609, E.610, Q.635 Chain C: Q.823 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, N.697, I.1117, G.1118 Chain C: 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: 4 residues within 4Å: Chain A: Y.342, I.459 Chain B: N.155, N.156 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: K.549 Chain B: N.271, E.272, N.273, T.277 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: F.329, G.330, N.334, L.359, N.361, S.362 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.8, T.10, N.128, D.129 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: Y.19, F.50, N.52, P.622 Ligand excluded by PLIP NAG.42: 9 residues within 4Å: Chain C: N.113, T.115, N.116, V.118, K.120, F.148, Y.151, V.162, P.165 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.322, Q.571 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.594 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain A: Q.823 Chain C: N.607, T.609, E.610, Q.635 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain A: D.783 Chain C: N.696, N.697, I.1117, G.1118 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain A: Q.882 Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain C: N.1085, G.1086, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain B: Y.342, I.459 Chain C: N.155, N.156 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain B: K.549 Chain C: N.271, E.272, N.273, T.277 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain C: F.329, G.330, N.334, L.359, N.361, S.362 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.8, T.10, N.128, D.129 Ligand excluded by PLIP

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

BLA.26: 17 residues within 4Å: Chain A: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, F.166, M.168, R.181, F.183, I.194, S.196, H.198, L.217 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.90, A:I.110, A:N.112, A:V.117, A:L.217 Hydrogen bonds: A:N.112, A:R.181 Salt bridges: A:R.181, A:H.198 pi-Cation interactions: A:H.198 BLA.40: 17 residues within 4Å: Chain B: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, F.166, M.168, R.181, F.183, I.194, S.196, H.198, L.217 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.110, B:N.112, B:V.117, B:L.217 Hydrogen bonds: B:N.112, B:R.181 Salt bridges: B:R.181, B:H.198 pi-Cation interactions: B:H.198 BLA.54: 17 residues within 4Å: Chain C: N.90, I.92, R.93, G.94, W.95, I.110, V.111, N.112, V.117, F.166, M.168, R.181, F.183, I.194, S.196, H.198, L.217 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:N.90, C:I.110, C:N.112, C:V.117, C:L.217 Hydrogen bonds: C:N.112, C:R.181 Salt bridges: C:R.181, C:H.198 pi-Cation interactions: C:H.198

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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