SMTL ID : 6cs0.1

SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, one S1 CTD in an upwards conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: 2 residues within 4Å: Chain A: N.256 Chain C: R.531 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.686, N.888, Q.891, K.898 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain A: R.531 Chain B: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain B: R.302, N.305, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 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-BMA.11: 4 residues within 4Å: Chain B: Y.765, N.770, S.772, Q.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain A: L.818 Chain C: N.589, Q.617 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain C: Y.765, N.770, S.772, Q.773, S.901 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 5 residues within 4Å: Chain C: N.1067, T.1069, F.1072, P.1081, I.1083 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.1083

1 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: 5 residues within 4Å: Chain A: N.589, T.591, Q.617 Chain B: L.818, C.820 No protein-ligand interaction detected (PLIP)

8 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: 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.5: 4 residues within 4Å: Chain A: N.1067, T.1069, F.1072, P.1081 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: D.1096, N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.589, T.591 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: E.1041, R.1042, N.1043 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.106, T.108, N.109, I.151 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: R.531 Chain C: D.254, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 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.16: 4 residues within 4Å: Chain C: N.686, Q.891, N.894, Q.895 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.894, C:Q.895 Hydrogen bonds: C:Q.895

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

NAG.20: 1 residues within 4Å: Chain A: N.52 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.576 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.678, I.1099 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.1041, R.1042, N.1043 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Q.19, N.52 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.576 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.678 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.1067, S.1070 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1103 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: Q.19, N.52 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.214 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: P.304, N.305, P.552, K.553 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.576 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.678 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: E.1041, R.1042, N.1043 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

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