SMTL ID : 6zgf.1

Spike Protein of RaTG13 Bat Coronavirus in Closed Conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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: N.61, F.90, D.246 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.153, T.155, N.156, Q.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.156 NAG-NAG.3: 2 residues within 4Å: Chain A: N.196 Chain C: Y.382 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: T.139, N.265, T.267 Chain C: R.488, K.489, N.491, K.493, E.496 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.267 NAG-NAG.7: 3 residues within 4Å: Chain A: N.1125, T.1127, F.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1161 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.828, S.830, Q.831 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.61, F.90, D.246 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.153, T.155, N.156, Q.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.156 NAG-NAG.13: 2 residues within 4Å: Chain A: Y.382 Chain B: N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain A: R.488, K.489, N.491, K.493, E.496 Chain B: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.267 NAG-NAG.17: 3 residues within 4Å: Chain B: N.1125, T.1127, F.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1161 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.828, S.830, Q.831 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.61, F.90, D.246 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: N.153, T.155, N.156, Q.204 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.156 NAG-NAG.23: 2 residues within 4Å: Chain B: Y.382 Chain C: N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 8 residues within 4Å: Chain B: R.488, K.489, N.491, K.493, E.496 Chain C: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.267 NAG-NAG.27: 3 residues within 4Å: Chain C: N.1125, T.1127, F.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 1 residues within 4Å: Chain C: N.1161 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.828, S.830, Q.831 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 2 residues within 4Å: Chain A: N.362, Q.611 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 2 residues within 4Å: Chain B: N.362, Q.611 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.25: 2 residues within 4Å: Chain C: N.362, Q.611 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.744, L.949, Q.953 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.949 NAG-NAG-BMA.16: 3 residues within 4Å: Chain B: N.744, L.949, Q.953 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.949 NAG-NAG-BMA.26: 3 residues within 4Å: Chain C: N.744, L.949, Q.953 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.949

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.10: 4 residues within 4Å: Chain A: N.401 Chain C: F.487, Y.520, Y.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.401 NAG-FUC.20: 4 residues within 4Å: Chain A: F.487, Y.520, Y.524 Chain B: N.401 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.401 NAG-FUC.30: 4 residues within 4Å: Chain B: F.487, Y.520, Y.524 Chain C: N.401 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.401

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

NAG.31: 2 residues within 4Å: Chain A: N.48, N.168 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.92 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.311, E.312, N.313 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: G.370, E.371, N.374 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.647, T.649 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.736, G.1158 Chain B: D.823 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: A.733, E.1099, N.1101 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.48, N.168 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.92 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.311, E.312, N.313 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: G.370, E.371, N.374 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.647, T.649 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.736, G.1158 Chain C: D.823 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: A.733, E.1099, N.1101 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.634 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.688 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.48, N.168 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.92 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.311, E.312, N.313 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: G.370, E.371, N.374 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.647, T.649 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain A: D.823 Chain C: N.736, G.1158 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: A.733, E.1099, N.1101 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.634 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein