- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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
- 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: N.243, S.245, A.250, N.251, F.269
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.4: 8 residues within 4Å:- Chain A: R.567, V.569, S.570, Q.821, Y.925, N.930, L.953
- Ligands: NAG.23
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.570, A:Q.821
NAG-NAG-BMA.6: 5 residues within 4Å:- Chain B: N.243, S.245, A.250, N.251, F.269
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.8: 8 residues within 4Å:- Chain B: R.567, V.569, S.570, Q.821, Y.925, N.930, L.953
- Ligands: NAG.39
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.570, B:Q.821
NAG-NAG-BMA.10: 5 residues within 4Å:- Chain C: N.243, S.245, A.250, N.251, F.269
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.12: 8 residues within 4Å:- Chain C: R.567, V.569, S.570, Q.821, Y.925, N.930, L.953
- Ligands: NAG.55
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:S.570, C:Q.821
- 3 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: 3 residues within 4Å:- Chain A: G.523, S.525, N.538
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 3 residues within 4Å:- Chain B: G.523, S.525, N.538
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 3 residues within 4Å:- Chain C: G.523, S.525, N.538
No protein-ligand interaction detected (PLIP)- 48 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.13: 2 residues within 4Å:- Chain A: Y.96, N.98
Ligand excluded by PLIPNAG.14: 3 residues within 4Å:- Chain A: N.122, T.227, C.230
Ligand excluded by PLIPNAG.15: 4 residues within 4Å:- Chain A: V.142, Y.144, N.171, T.178
Ligand excluded by PLIPNAG.16: 3 residues within 4Å:- Chain A: R.129, A.155, N.220
Ligand excluded by PLIPNAG.17: 2 residues within 4Å:- Chain A: D.307, N.326
Ligand excluded by PLIPNAG.18: 1 residues within 4Å:- Chain A: N.518
Ligand excluded by PLIPNAG.19: 1 residues within 4Å:- Chain A: N.440
Ligand excluded by PLIPNAG.20: 2 residues within 4Å:- Chain A: N.464, D.465
Ligand excluded by PLIPNAG.21: 2 residues within 4Å:- Chain A: N.663, S.665
Ligand excluded by PLIPNAG.22: 2 residues within 4Å:- Chain A: N.542, T.544
Ligand excluded by PLIPNAG.23: 4 residues within 4Å:- Chain A: Q.565, N.568
- Chain C: K.656
- Ligands: NAG-NAG-BMA.4
Ligand excluded by PLIPNAG.24: 3 residues within 4Å:- Chain A: N.581, D.959, E.961
Ligand excluded by PLIPNAG.25: 6 residues within 4Å:- Chain A: N.587, W.588, E.789, I.793, T.955, Q.956
Ligand excluded by PLIPNAG.26: 1 residues within 4Å:- Chain A: N.671
Ligand excluded by PLIPNAG.27: 5 residues within 4Å:- Chain A: N.1015, T.1017, F.1018
- Chain C: L.771, Q.788
Ligand excluded by PLIPNAG.28: 2 residues within 4Å:- Chain A: V.1016, N.1020
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain B: Y.96, N.98
Ligand excluded by PLIPNAG.30: 3 residues within 4Å:- Chain B: N.122, T.227, C.230
Ligand excluded by PLIPNAG.31: 4 residues within 4Å:- Chain B: V.142, Y.144, N.171, T.178
Ligand excluded by PLIPNAG.32: 3 residues within 4Å:- Chain B: R.129, A.155, N.220
Ligand excluded by PLIPNAG.33: 2 residues within 4Å:- Chain B: D.307, N.326
Ligand excluded by PLIPNAG.34: 1 residues within 4Å:- Chain B: N.518
Ligand excluded by PLIPNAG.35: 1 residues within 4Å:- Chain B: N.440
Ligand excluded by PLIPNAG.36: 2 residues within 4Å:- Chain B: N.464, D.465
Ligand excluded by PLIPNAG.37: 2 residues within 4Å:- Chain B: N.663, S.665
Ligand excluded by PLIPNAG.38: 2 residues within 4Å:- Chain B: N.542, T.544
Ligand excluded by PLIPNAG.39: 4 residues within 4Å:- Chain A: K.656
- Chain B: Q.565, N.568
- Ligands: NAG-NAG-BMA.8
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain B: N.581, D.959
Ligand excluded by PLIPNAG.41: 5 residues within 4Å:- Chain B: N.587, W.588, I.793, T.955, Q.956
Ligand excluded by PLIPNAG.42: 1 residues within 4Å:- Chain B: N.671
Ligand excluded by PLIPNAG.43: 5 residues within 4Å:- Chain A: L.771, Q.788
- Chain B: N.1015, T.1017, F.1018
Ligand excluded by PLIPNAG.44: 2 residues within 4Å:- Chain B: V.1016, N.1020
Ligand excluded by PLIPNAG.45: 2 residues within 4Å:- Chain C: Y.96, N.98
Ligand excluded by PLIPNAG.46: 3 residues within 4Å:- Chain C: N.122, T.227, C.230
Ligand excluded by PLIPNAG.47: 4 residues within 4Å:- Chain C: V.142, Y.144, N.171, T.178
Ligand excluded by PLIPNAG.48: 3 residues within 4Å:- Chain C: R.129, A.155, N.220
Ligand excluded by PLIPNAG.49: 2 residues within 4Å:- Chain C: D.307, N.326
Ligand excluded by PLIPNAG.50: 1 residues within 4Å:- Chain C: N.518
Ligand excluded by PLIPNAG.51: 1 residues within 4Å:- Chain C: N.440
Ligand excluded by PLIPNAG.52: 2 residues within 4Å:- Chain C: N.464, D.465
Ligand excluded by PLIPNAG.53: 2 residues within 4Å:- Chain C: N.663, S.665
Ligand excluded by PLIPNAG.54: 2 residues within 4Å:- Chain C: N.542, T.544
Ligand excluded by PLIPNAG.55: 4 residues within 4Å:- Chain B: K.656
- Chain C: Q.565, N.568
- Ligands: NAG-NAG-BMA.12
Ligand excluded by PLIPNAG.56: 2 residues within 4Å:- Chain C: N.581, D.959
Ligand excluded by PLIPNAG.57: 5 residues within 4Å:- Chain C: N.587, W.588, I.793, T.955, Q.956
Ligand excluded by PLIPNAG.58: 1 residues within 4Å:- Chain C: N.671
Ligand excluded by PLIPNAG.59: 5 residues within 4Å:- Chain B: L.771, Q.788
- Chain C: N.1015, T.1017, F.1018
Ligand excluded by PLIPNAG.60: 2 residues within 4Å:- Chain C: V.1016, N.1020
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Song, X. et al., Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun (2021)
- Release Date
- 2020-12-23
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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
- 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
- 3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 48 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Song, X. et al., Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun (2021)
- Release Date
- 2020-12-23
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C