SMTL ID : 6crx.1

SARS Spike Glycoprotein, Stabilized variant, two S1 CTDs in the upwards conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

19 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.589, T.591 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: Y.50, N.52 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1067, T.1069, S.1070, F.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: R.302, N.305, I.306, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: Q.19, N.52 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.214 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.305, K.553 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: Y.765, N.770, Q.773, F.786 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.786 NAG-NAG.14: 3 residues within 4Å: Chain B: S.673, N.1043 Chain C: Q.864 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.673, B:S.673 NAG-NAG.15: 5 residues within 4Å: Chain B: N.1067, T.1069, S.1070, W.1071, F.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain A: R.531 Chain B: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: R.531 Chain C: D.254, E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.305, K.553 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: E.281, N.576 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: S.677, N.678, I.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain A: Q.864 Chain C: A.675, N.1043 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.1067, G.1068, T.1069, F.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain C: N.1103 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.3: 3 residues within 4Å: Chain A: E.255, N.256 Chain C: R.531 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: N.686, Q.891, N.894, Q.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.891, A:N.894 NAG-NAG-BMA.23: 5 residues within 4Å: Chain C: N.686, Q.891, N.894, Q.895, K.898 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.894 Hydrogen bonds: C:N.894

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

NAG-NAG-BMA-MAN.4: 5 residues within 4Å: Chain A: Y.765, N.770, S.772, Q.773, D.777 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 2 residues within 4Å: Chain B: N.589 Chain C: I.819 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 2 residues within 4Å: Chain B: N.686, Q.891 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 5 residues within 4Å: Chain A: L.818, C.820 Chain C: N.589, T.591, Q.617 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 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

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

NAG.28: 1 residues within 4Å: Chain A: N.576 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain A: N.678, G.1100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.678 NAG.30: 1 residues within 4Å: Chain A: N.1043 No protein-ligand interaction detected (PLIP) NAG.31: 5 residues within 4Å: Chain A: C.1051, C.1095, D.1096, I.1101, N.1103 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.1101 NAG.32: 1 residues within 4Å: Chain B: N.576 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.576 NAG.33: 1 residues within 4Å: Chain B: N.678 No protein-ligand interaction detected (PLIP) NAG.34: 3 residues within 4Å: Chain C: Q.19, T.21, N.52 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.19 Hydrogen bonds: C:N.52

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
B

B
C

C
A

Spike glycoprotein,Fibritin

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