SMTL ID : 6cs1.1

SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, two S1 CTDs in an upwards 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: 4 residues within 4Å: Chain A: D.254, E.255, N.256 Chain C: R.531 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: D.283, N.576 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: N.1067, T.1069, S.1070, W.1071, F.1072, I.1083 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1083 Hydrogen bonds: A:S.1070 NAG-NAG.7: 4 residues within 4Å: Chain A: N.589, T.591 Chain B: I.819, C.820 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.52 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.305, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 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.20: 3 residues within 4Å: Chain C: N.1067, T.1069, F.1072 No protein-ligand interaction detected (PLIP)

6 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: R.302, N.305, I.306, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain A: R.531 Chain B: D.254, E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain B: N.1067, T.1069, S.1070, W.1071, F.1072, P.1081, I.1083 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.1083 NAG-NAG-BMA.18: 4 residues within 4Å: Chain C: N.686, Q.891, N.894, Q.895 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.894, C:Q.895 Hydrogen bonds: C:N.894, C:K.898, C:K.898 NAG-NAG-BMA.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 NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: N.305, K.553 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.4: 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.891 NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain A: Y.765, N.770, S.772, Q.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 3 residues within 4Å: Chain B: R.531 Chain C: E.255, N.256 No protein-ligand interaction detected (PLIP)

3 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.11: 4 residues within 4Å: Chain B: N.589, T.591 Chain C: I.819, C.820 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 6 residues within 4Å: Chain B: N.686, F.687, Q.891, N.894, Q.895, Q.1040 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.891 NAG-NAG-BMA-MAN.13: 3 residues within 4Å: Chain B: N.770, S.772, Q.773 No protein-ligand interaction detected (PLIP)

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

NAG.22: 3 residues within 4Å: Chain A: A.675, N.1043 Chain B: Q.864 No protein-ligand interaction detected (PLIP) NAG.23: 3 residues within 4Å: Chain A: Q.19, Y.50, N.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.52 NAG.24: 4 residues within 4Å: Chain A: C.1051, C.1095, D.1096, N.1103 No protein-ligand interaction detected (PLIP) NAG.25: 1 residues within 4Å: Chain A: N.678 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.678 NAG.26: 1 residues within 4Å: Chain B: N.576 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.576 NAG.27: 3 residues within 4Å: Chain B: E.1041, R.1042, N.1043 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.1042 Hydrogen bonds: B:N.1043 NAG.28: 2 residues within 4Å: Chain B: N.678, I.1099 No protein-ligand interaction detected (PLIP) NAG.29: 5 residues within 4Å: Chain C: Q.19, T.21, Y.50, N.52, R.607 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.19 Hydrogen bonds: C:N.52, C:R.607 NAG.30: 1 residues within 4Å: Chain C: N.576 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.576 NAG.31: 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 NAG.32: 1 residues within 4Å: Chain C: N.1103 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain C: N.678 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.678

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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