SMTL ID : 6x79.1

Prefusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: 3 residues within 4Å: Chain A: T.127, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.255 NAG-NAG.2: 4 residues within 4Å: Chain A: N.736, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.941, A:N.944 NAG-NAG.3: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: T.127, N.253, T.255 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.255 NAG-NAG.5: 4 residues within 4Å: Chain B: N.736, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.941, B:N.944 NAG-NAG.6: 3 residues within 4Å: Chain B: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: T.127, N.253, T.255 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.255 NAG-NAG.8: 4 residues within 4Å: Chain C: N.736, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.941, C:N.944 NAG-NAG.9: 3 residues within 4Å: Chain C: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP)

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

NAG.10: 1 residues within 4Å: Chain A: N.141 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.299, E.300, N.301 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.350, P.598, Q.599 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: F.357, G.358, N.362, V.386, L.387 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: H.674, V.675, N.676 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.1117, T.1119, F.1122 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: I.1151, N.1153 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.141 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.299, E.300, N.301 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.350, P.598, Q.599 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: F.357, G.358, N.362, V.386, L.387 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.635, Q.663 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: H.674, V.675, N.676 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.1117, T.1119, F.1122 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: I.1151, N.1153 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.141 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.299, E.300, N.301 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.350, P.598, Q.599 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: F.357, G.358, N.362, V.386, L.387 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.635, Q.663 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: H.674, V.675, N.676 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.1117, T.1119, F.1122 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: I.1151, N.1153 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.622 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-08-19

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein