SMTL ID : 6zoz.1

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Locked State

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: 5 residues within 4Å: Chain A: N.225, T.227 Chain C: R.448, N.451, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.704, F.705, L.909 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.3: 2 residues within 4Å: Chain A: N.788, S.790 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: 5 residues within 4Å: Chain A: R.448, N.451, E.456 Chain B: N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.704, F.705, L.909 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.909 NAG-NAG.7: 2 residues within 4Å: Chain B: N.788, S.790 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: 5 residues within 4Å: Chain B: R.448, N.451, E.456 Chain C: N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.704, F.705, L.909 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.11: 2 residues within 4Å: Chain C: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.21, N.52 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.113, T.115, N.116, V.118 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: 3 residues within 4Å: Chain A: N.607, T.609 Chain B: Q.823 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 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: 3 residues within 4Å: Chain A: N.156 Chain C: I.459, T.461 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.272, N.273 Chain C: K.549 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.334, V.358, 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.27: 2 residues within 4Å: Chain B: N.21, N.52 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.113, T.115, N.116, V.118 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.594 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.607, T.609 Chain C: Q.823 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: I.459, T.461 Chain B: N.156 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: K.549 Chain B: E.272, N.273 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.334, V.358, 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.41: 2 residues within 4Å: Chain C: N.21, N.52 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.113, T.115, N.116, V.118 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: 3 residues within 4Å: Chain A: Q.823 Chain C: N.607, T.609 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: I.459, T.461 Chain C: N.156 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: K.549 Chain C: E.272, N.273 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.334, V.358, S.362 Ligand excluded by PLIP NAG.53: 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: 8 residues within 4Å: Chain A: N.90, I.92, I.110, N.112, V.117, R.181, F.183, L.217 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.90, A:I.110, A:N.112, A:V.117, A:L.217, A:L.217 Hydrogen bonds: A:N.112 pi-Cation interactions: A:R.181, A:H.198 BLA.40: 8 residues within 4Å: Chain B: N.90, I.92, I.110, N.112, V.117, R.181, F.183, L.217 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.90, B:I.110, B:N.112, B:V.117, B:L.217, B:L.217 Hydrogen bonds: B:N.112 pi-Cation interactions: B:R.181, B:H.198 BLA.54: 8 residues within 4Å: Chain C: N.90, I.92, I.110, N.112, V.117, R.181, F.183, L.217 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.90, C:I.110, C:N.112, C:V.117, C:L.217, C:L.217 Hydrogen bonds: C:N.112 pi-Cation interactions: C:R.181, C:H.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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