- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 21 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: 9 residues within 4Å:- Chain A: D.28, F.29, N.30, I.142, N.143
- Chain C: Y.450, S.453, R.457
- Ligands: NAG.41
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.30, A:N.30
NAG-NAG-BMA.4: 3 residues within 4Å:- Chain A: H.153, E.158, N.199
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.5: 2 residues within 4Å:- Chain A: V.675, N.677
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.6: 3 residues within 4Å:- Chain A: N.203, S.205, T.206
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.8: 3 residues within 4Å:- Chain A: N.69, D.283, R.947
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.10: 6 residues within 4Å:- Chain A: F.725, D.726, S.727, N.737, T.739, D.740
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.740
NAG-NAG-BMA.11: 2 residues within 4Å:- Chain A: F.347, N.444
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.14: 8 residues within 4Å:- Chain A: Y.450, R.457
- Chain B: D.28, F.29, N.30, I.142, N.143
- Ligands: NAG.51
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.30, B:N.30
NAG-NAG-BMA.16: 3 residues within 4Å:- Chain B: H.153, E.158, N.199
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.17: 2 residues within 4Å:- Chain B: V.675, N.677
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.18: 3 residues within 4Å:- Chain B: N.203, S.205, T.206
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.20: 3 residues within 4Å:- Chain B: N.69, D.283, R.947
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.22: 5 residues within 4Å:- Chain B: F.725, D.726, N.737, T.739, D.740
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.740
NAG-NAG-BMA.23: 2 residues within 4Å:- Chain B: F.347, N.444
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.26: 9 residues within 4Å:- Chain B: Y.450, S.453, R.457
- Chain C: D.28, F.29, N.30, I.142, N.143
- Ligands: NAG.61
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.30, C:N.30
NAG-NAG-BMA.28: 4 residues within 4Å:- Chain C: H.153, E.158, K.175, N.199
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.29: 3 residues within 4Å:- Chain C: S.656, V.675, N.677
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.30: 3 residues within 4Å:- Chain C: N.203, S.205, T.206
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.32: 3 residues within 4Å:- Chain C: N.69, D.283, R.947
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.34: 6 residues within 4Å:- Chain C: F.725, D.726, S.727, N.737, T.739, D.740
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.740
NAG-NAG-BMA.35: 2 residues within 4Å:- Chain C: F.347, N.444
No protein-ligand interaction detected (PLIP)- 3 x SIA- 5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)
SIA-5N6.12: 10 residues within 4Å:- Chain A: N.37, L.39, T.41, T.93, T.94, K.95, L.96, S.97, S.257, N.259
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.37, A:T.93, A:S.257, A:N.259
- Salt bridges: A:K.91, A:K.95, A:K.95
SIA-5N6.24: 11 residues within 4Å:- Chain B: N.37, L.39, T.41, I.43, T.93, T.94, K.95, L.96, S.97, S.257, N.259
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:K.95
- Hydrogen bonds: B:N.37, B:T.93, B:S.257, B:N.259
- Salt bridges: B:K.91, B:K.95, B:K.95
SIA-5N6.36: 10 residues within 4Å:- Chain C: N.37, L.39, T.41, T.93, T.94, K.95, L.96, S.97, W.100, S.257
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:N.37, C:T.93, C:S.257
- Salt bridges: C:K.91, C:K.95, C:K.95
- 30 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.37: 3 residues within 4Å:- Chain A: D.630, N.715, N.716
Ligand excluded by PLIPNAG.38: 2 residues within 4Å:- Chain A: N.808, I.1166
Ligand excluded by PLIPNAG.39: 8 residues within 4Å:- Chain A: D.337, N.364, N.366, N.618, D.619
- Chain C: A.538, Y.539, P.541
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain A: R.181, N.182
Ligand excluded by PLIPNAG.41: 3 residues within 4Å:- Chain A: N.30, N.33
- Ligands: NAG-NAG-BMA.2
Ligand excluded by PLIPNAG.42: 5 residues within 4Å:- Chain A: N.481, F.484, C.544, S.545, K.547
Ligand excluded by PLIPNAG.43: 1 residues within 4Å:- Chain A: N.465
Ligand excluded by PLIPNAG.44: 3 residues within 4Å:- Chain A: L.570, S.573, N.575
Ligand excluded by PLIPNAG.45: 5 residues within 4Å:- Chain A: S.742, V.743, S.744, E.783, N.786
Ligand excluded by PLIPNAG.46: 1 residues within 4Å:- Chain A: N.791
Ligand excluded by PLIPNAG.47: 3 residues within 4Å:- Chain B: D.630, N.715, N.716
Ligand excluded by PLIPNAG.48: 2 residues within 4Å:- Chain B: N.808, I.1166
Ligand excluded by PLIPNAG.49: 8 residues within 4Å:- Chain A: A.538, Y.539, P.541
- Chain B: D.337, N.364, N.366, N.618, D.619
Ligand excluded by PLIPNAG.50: 2 residues within 4Å:- Chain B: R.181, N.182
Ligand excluded by PLIPNAG.51: 3 residues within 4Å:- Chain B: N.30, N.33
- Ligands: NAG-NAG-BMA.14
Ligand excluded by PLIPNAG.52: 5 residues within 4Å:- Chain B: N.481, F.484, C.544, S.545, K.547
Ligand excluded by PLIPNAG.53: 1 residues within 4Å:- Chain B: N.465
Ligand excluded by PLIPNAG.54: 4 residues within 4Å:- Chain B: V.569, L.570, S.573, N.575
Ligand excluded by PLIPNAG.55: 5 residues within 4Å:- Chain B: S.742, V.743, S.744, E.783, N.786
Ligand excluded by PLIPNAG.56: 1 residues within 4Å:- Chain B: N.791
Ligand excluded by PLIPNAG.57: 3 residues within 4Å:- Chain C: D.630, N.715, N.716
Ligand excluded by PLIPNAG.58: 2 residues within 4Å:- Chain C: N.808, I.1166
Ligand excluded by PLIPNAG.59: 7 residues within 4Å:- Chain B: A.538, Y.539
- Chain C: D.337, N.364, N.366, N.618, D.619
Ligand excluded by PLIPNAG.60: 2 residues within 4Å:- Chain C: R.181, N.182
Ligand excluded by PLIPNAG.61: 3 residues within 4Å:- Chain C: N.30, N.33
- Ligands: NAG-NAG-BMA.26
Ligand excluded by PLIPNAG.62: 5 residues within 4Å:- Chain C: N.481, F.484, C.544, S.545, K.547
Ligand excluded by PLIPNAG.63: 1 residues within 4Å:- Chain C: N.465
Ligand excluded by PLIPNAG.64: 4 residues within 4Å:- Chain C: V.569, L.570, S.573, N.575
Ligand excluded by PLIPNAG.65: 5 residues within 4Å:- Chain C: S.742, V.743, S.744, E.783, N.786
Ligand excluded by PLIPNAG.66: 1 residues within 4Å:- Chain C: N.791
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pronker, M.F. et al., Sialoglycan binding triggers spike opening in a human coronavirus. Nature (2023)
- Release Date
- 2023-08-02
- Peptides
- Spike glycoprotein,General control transcription factor GCN4: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 21 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
- 3 x SIA- 5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)
- 30 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pronker, M.F. et al., Sialoglycan binding triggers spike opening in a human coronavirus. Nature (2023)
- Release Date
- 2023-08-02
- Peptides
- Spike glycoprotein,General control transcription factor GCN4: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C