SMTL ID : 6crv.1

SARS Spike Glycoprotein, Stabilized variant, C3 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 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: 2 residues within 4Å: Chain A: N.256 Chain C: R.531 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.531 NAG-NAG.3: 4 residues within 4Å: Chain A: N.686, Q.891, Q.895, Q.1040 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.895 NAG-NAG.4: 2 residues within 4Å: Chain A: R.531 Chain B: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.531 NAG-NAG.6: 4 residues within 4Å: Chain B: N.686, Q.891, Q.895, Q.1040 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.895 NAG-NAG.7: 2 residues within 4Å: Chain B: R.531 Chain C: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.686, Q.891, Q.895, Q.1040 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.895

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.2: 5 residues within 4Å: Chain A: Y.765, N.770, S.772, Q.773, F.786 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.786 NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: Y.765, N.770, S.772, Q.773, F.786 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.786 NAG-NAG-BMA.8: 5 residues within 4Å: Chain C: Y.765, N.770, S.772, Q.773, F.786 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.786

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

NAG.10: 2 residues within 4Å: Chain A: Q.19, N.52 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.678, I.1099 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.1067, T.1069, F.1072 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1103 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: A.675, E.1041, N.1043 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.589, T.591, Q.617 Chain B: L.818, C.820 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: Q.19, N.52 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.678, I.1099 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.1067, T.1069, F.1072 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1103 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: A.675, E.1041, N.1043 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: N.589, T.591, Q.617 Chain C: L.818, C.820 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: Q.19, N.52 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.678, I.1099 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.1067, T.1069, F.1072 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.1103 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: A.675, E.1041, N.1043 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: L.818, C.820 Chain C: N.589, T.591, Q.617 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirchdoerfer, R.N. et al., Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Sci Rep (2018)

Release Date

2018-04-11

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin