SMTL ID : 6crw.1

SARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

5 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.1: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain B: E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain B: N.305, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain B: N.686, F.687, Q.891, N.894, Q.895 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.894 Hydrogen bonds: B:Q.891 NAG-NAG-BMA.20: 5 residues within 4Å: Chain C: N.1067, T.1069, S.1070, F.1072, P.1081 No protein-ligand interaction detected (PLIP)

6 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.2: 4 residues within 4Å: Chain A: N.589, T.591, Q.617 Chain B: L.818 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain A: N.686, Q.891, K.898 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 4 residues within 4Å: Chain B: Y.765, N.770, S.772, Q.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 5 residues within 4Å: Chain C: N.106, T.108, N.109, I.151, A.154 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.154 Hydrogen bonds: C:N.109 NAG-NAG-BMA-MAN.17: 4 residues within 4Å: Chain A: L.818 Chain C: N.589, T.591, Q.617 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.19: 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

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.4: 4 residues within 4Å: Chain A: N.770, S.772, Q.773, F.786 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.786 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: 1 residues within 4Å: Chain A: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: Q.19, N.52 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.589, T.591 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: A.675, R.1042, N.1043 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.675 NAG-NAG.14: 1 residues within 4Å: Chain B: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: R.531 Chain C: E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.1103 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.18: 3 residues within 4Å: Chain C: N.686, F.687, Q.895 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.895

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

NAG.22: 2 residues within 4Å: Chain A: Q.19, N.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.52 NAG.23: 1 residues within 4Å: Chain A: N.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.576 NAG.24: 1 residues within 4Å: Chain A: N.678 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.678, A:N.678 NAG.25: 2 residues within 4Å: Chain A: N.1043 Chain B: Q.864 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.1043, B:Q.864 NAG.26: 1 residues within 4Å: Chain B: N.576 No protein-ligand interaction detected (PLIP) NAG.27: 2 residues within 4Å: Chain B: N.678, I.1099 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.1099 Hydrogen bonds: B:N.678 NAG.28: 2 residues within 4Å: Chain B: N.1067, S.1070 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.1067, B:S.1070 NAG.29: 2 residues within 4Å: Chain C: Q.19, N.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.52 NAG.30: 1 residues within 4Å: Chain C: N.214 No protein-ligand interaction detected (PLIP) NAG.31: 3 residues within 4Å: Chain C: N.305, P.552, K.553 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.553 NAG.32: 1 residues within 4Å: Chain C: N.576 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.576 NAG.33: 1 residues within 4Å: Chain C: N.678 No protein-ligand interaction detected (PLIP) NAG.34: 3 residues within 4Å: Chain C: E.1041, R.1042, N.1043 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1043

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

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