SMTL ID : 6zox.1

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x2 disulphide-bond mutant, G413C, V987C, single Arg S1/S2 cleavage site)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: T.99, N.225, T.227 Chain C: R.448, S.450 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.3: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: R.448, S.450 Chain B: T.99, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.909 NAG-NAG.8: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: R.448, S.450 Chain C: T.99, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.13: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.19, N.52 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.113, T.115, N.116, E.145 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.273 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.322, Q.571 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: F.329, G.330, N.334 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.594 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.607 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.696 Chain B: I.781, D.783 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.155, N.156 Chain C: Y.342 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.19, N.52 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.113, T.115, N.116, E.145 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.273 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: F.329, G.330, N.334 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.594 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.607 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.696 Chain C: I.781, D.783 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: Y.342 Chain B: N.155, N.156 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.19, N.52 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.113, T.115, N.116, E.145 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.273 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.322, Q.571 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: F.329, G.330, N.334 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.594 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.607 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: I.781, D.783 Chain C: N.696 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: Y.342 Chain C: N.155, N.156 Ligand excluded by PLIP

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