- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 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
- 12 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: 10 residues within 4Å:- Chain A: A.232, N.233, C.234, I.235, G.236, N.258, K.289, I.323, N.324, W.439
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.289, A:N.233, A:K.289
NAG-NAG-BMA.3: 5 residues within 4Å:- Chain A: N.726, S.727, N.739, D.740, S.759
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.4: 6 residues within 4Å:- Chain A: L.504, D.640, N.688, V.689, T.690, S.691
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:D.640
NAG-NAG-BMA.8: 8 residues within 4Å:- Chain A: T.137, A.138, N.140, T.143, N.873, T.875, N.876, F.896
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.137, A:N.140, A:N.140
NAG-NAG-BMA.14: 6 residues within 4Å:- Chain B: Q.42, N.324, D.325, R.396, D.432, D.433
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.42
NAG-NAG-BMA.17: 2 residues within 4Å:- Chain B: Y.184, N.425
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:Y.184
NAG-NAG-BMA.19: 6 residues within 4Å:- Chain B: V.502, D.640, M.644, N.688, T.690, S.691
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.21: 4 residues within 4Å:- Chain B: N.781, D.1165
- Chain C: T.967, A.969
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.27: 7 residues within 4Å:- Chain C: Q.42, N.324, D.325, R.396, D.432, D.433, D.434
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Q.42, C:Q.42
NAG-NAG-BMA.30: 3 residues within 4Å:- Chain C: Y.184, G.333, N.425
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:Y.184
NAG-NAG-BMA.31: 6 residues within 4Å:- Chain C: D.640, S.642, M.644, N.688, T.690, S.691
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.33: 3 residues within 4Å:- Chain C: N.873, T.875, N.876
No protein-ligand interaction detected (PLIP)- 10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-NAG.5: 1 residues within 4Å:- Chain A: N.743
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 2 residues within 4Å:- Chain A: N.781
- Chain B: A.969
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 5 residues within 4Å:- Chain A: T.786, N.787, R.994, N.995, D.1162
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 4 residues within 4Å:- Chain A: D.1176, V.1228, Y.1230, N.1232
No protein-ligand interaction detected (PLIP)NAG-NAG.15: 6 residues within 4Å:- Chain B: F.296, H.338, G.342, T.343, N.344, D.378
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 2 residues within 4Å:- Chain B: N.726, N.739
No protein-ligand interaction detected (PLIP)NAG-NAG.20: 4 residues within 4Å:- Chain B: R.729, N.743, Y.764
- Chain C: R.887
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:R.887
- Hydrophobic interactions: B:Y.764
NAG-NAG.22: 3 residues within 4Å:- Chain B: N.873, T.875, N.876
No protein-ligand interaction detected (PLIP)NAG-NAG.28: 5 residues within 4Å:- Chain C: H.338, G.342, T.343, N.344, D.378
No protein-ligand interaction detected (PLIP)NAG-NAG.32: 2 residues within 4Å:- Chain A: A.969
- Chain C: N.781
No protein-ligand interaction detected (PLIP)- 2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-FUC.10: 6 residues within 4Å:- Chain A: A.43, M.214, N.216, T.218, S.226, Q.228
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:T.218
- Hydrogen bonds: A:N.216, A:S.226, A:S.226, A:Q.228
NAG-NAG-FUC.23: 5 residues within 4Å:- Chain B: D.1176, V.1228, T.1229, Y.1230, N.1232
No protein-ligand interaction detected (PLIP)- 3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-BMA-FUC.11: 5 residues within 4Å:- Chain B: M.214, N.216, T.218, G.224, S.226
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:T.218
NAG-NAG-BMA-FUC.24: 4 residues within 4Å:- Chain C: M.214, N.216, T.218, S.226
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-FUC.34: 6 residues within 4Å:- Chain C: D.1176, C.1226, V.1227, V.1228, Y.1230, N.1232
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:D.1176, C:N.1232
- 4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-FUC.13: 2 residues within 4Å:- Chain B: N.300, Q.301
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.301, B:Q.301
NAG-FUC.16: 3 residues within 4Å:- Chain B: N.351, P.363, L.364
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:N.351
NAG-FUC.26: 3 residues within 4Å:- Chain C: N.300, Q.301, A.315
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Q.301
- Hydrophobic interactions: C:A.315
NAG-FUC.29: 4 residues within 4Å:- Chain C: N.351, S.352, P.363, L.364
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:P.363
- 18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.35: 2 residues within 4Å:- Chain A: N.300, Q.301
Ligand excluded by PLIPNAG.36: 4 residues within 4Å:- Chain A: G.294, F.296, N.425, H.429
Ligand excluded by PLIPNAG.37: 4 residues within 4Å:- Chain A: F.296, H.338, G.342, N.344
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain A: T.666, N.667
- Chain B: R.924
Ligand excluded by PLIPNAG.39: 3 residues within 4Å:- Chain A: S.1005, A.1006, N.1009
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain A: Y.380, N.381
Ligand excluded by PLIPNAG.41: 3 residues within 4Å:- Chain B: G.115, T.117, N.118
Ligand excluded by PLIPNAG.42: 3 residues within 4Å:- Chain B: T.379, Y.380, N.381
Ligand excluded by PLIPNAG.43: 4 residues within 4Å:- Chain B: L.665, T.666, N.667
- Chain C: R.924
Ligand excluded by PLIPNAG.44: 2 residues within 4Å:- Chain B: N.787, D.1162
Ligand excluded by PLIPNAG.45: 3 residues within 4Å:- Chain B: S.1005, A.1006, N.1009
Ligand excluded by PLIPNAG.46: 4 residues within 4Å:- Chain C: G.115, N.116, T.117, N.118
Ligand excluded by PLIPNAG.47: 4 residues within 4Å:- Chain C: F.512, N.514, N.537, S.552
Ligand excluded by PLIPNAG.48: 3 residues within 4Å:- Chain C: T.516, S.518, N.556
Ligand excluded by PLIPNAG.49: 3 residues within 4Å:- Chain C: L.665, T.666, N.667
Ligand excluded by PLIPNAG.50: 1 residues within 4Å:- Chain C: N.743
Ligand excluded by PLIPNAG.51: 2 residues within 4Å:- Chain C: N.787, D.1162
Ligand excluded by PLIPNAG.52: 3 residues within 4Å:- Chain C: S.1005, G.1008, N.1009
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, C.Y. et al., In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM. Nat Commun (2022)
- Release Date
- 2022-08-03
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
B
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-trimer
- Ligands
- 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
- 12 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
- 10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, C.Y. et al., In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM. Nat Commun (2022)
- Release Date
- 2022-08-03
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
B