SMTL ID : 6cs2.1

SARS Spike Glycoprotein - human ACE2 complex, Stabilized variant, all ACE2-bound particles

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

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: 3 residues within 4Å: Chain A: E.255, N.256 Chain C: R.531 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: N.305, K.553, S.555 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain A: N.589, T.591 Chain B: L.818, I.819, C.820 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 1 residues within 4Å: Chain B: N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: N.589 Chain C: L.818, I.819 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 4 residues within 4Å: Chain B: N.686, Q.891, N.894, Q.895 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.894 NAG-NAG-BMA.18: 1 residues within 4Å: Chain B: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain C: Q.19, N.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain B: R.531 Chain C: D.254, N.256 No protein-ligand interaction detected (PLIP)

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain A: N.678, I.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: S.673, I.674, A.675, N.1043 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.675 NAG-NAG.10: 2 residues within 4Å: Chain B: Q.19, N.52 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.678, N.679, I.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.305, K.553, T.554 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: N.678, I.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.1103 No protein-ligand interaction detected (PLIP)

10 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: N.686, Q.891, N.894, Q.895, Q.1040 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.894, A:Q.895 Hydrogen bonds: A:Q.891, A:N.894 NAG-NAG-BMA-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.7: 5 residues within 4Å: Chain A: N.1067, T.1069, F.1072, F.1079, P.1081 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 1 residues within 4Å: Chain A: N.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 2 residues within 4Å: Chain B: N.305, K.553 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 3 residues within 4Å: Chain B: Y.765, N.770, Q.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 4 residues within 4Å: Chain C: N.686, Q.891, N.894, Q.895 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.894 Hydrogen bonds: C:N.894 NAG-NAG-BMA-MAN.24: 4 residues within 4Å: Chain C: Y.765, N.770, S.772, Q.773 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 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.27: 3 residues within 4Å: Chain C: N.1067, T.1069, F.1072 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.17: 3 residues within 4Å: Chain B: N.1067, T.1069, F.1072 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain A: Q.19, N.52, R.607 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.19 Hydrogen bonds: A:R.607 NAG.29: 1 residues within 4Å: Chain A: N.576 No protein-ligand interaction detected (PLIP) NAG.30: 1 residues within 4Å: Chain B: N.576 No protein-ligand interaction detected (PLIP) NAG.31: 3 residues within 4Å: Chain B: E.1041, R.1042, N.1043 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1043 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.1043 No protein-ligand interaction detected (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
Angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein,Fibritin

Angiotensin-converting enzyme 2

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