- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 16 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 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: 4 residues within 4Å:- Chain A: N.717, L.922, Q.926, Q.1071
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.922
NAG-NAG-BMA-MAN.3: 4 residues within 4Å:- Chain A: N.801, S.803, Q.804
- Ligands: MAN.33
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-MAN.15: 4 residues within 4Å:- Chain B: N.717, L.922, Q.926, Q.1071
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:L.922
NAG-NAG-BMA-MAN.18: 2 residues within 4Å:- Chain C: N.1134
- Ligands: MAN.45
No protein-ligand interaction detected (PLIP)- 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.11: 1 residues within 4Å:- Chain B: N.1134
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.12: 2 residues within 4Å:- Chain B: A.706, N.1074
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.20: 3 residues within 4Å:- Chain C: A.706, E.1072, N.1074
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.22: 3 residues within 4Å:- Chain C: N.717, L.922, Q.1071
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.922
NAG-NAG-BMA.24: 3 residues within 4Å:- Chain A: K.558
- Chain C: E.281, N.282
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.25: 4 residues within 4Å:- Chain C: F.338, G.339, F.342, N.343
No protein-ligand interaction detected (PLIP)- 1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.28: 1 residues within 4Å:- Chain A: N.603
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain A: N.616, T.618
Ligand excluded by PLIPNAG.30: 3 residues within 4Å:- Chain A: N.122, T.124, V.127
Ligand excluded by PLIPNAG.31: 2 residues within 4Å:- Chain A: N.164, N.165
Ligand excluded by PLIPNAG.32: 3 residues within 4Å:- Chain A: T.108, N.234, T.236
Ligand excluded by PLIPNAG.34: 2 residues within 4Å:- Chain B: N.331, Q.580
Ligand excluded by PLIPNAG.35: 2 residues within 4Å:- Chain B: N.616, T.618
Ligand excluded by PLIPNAG.36: 1 residues within 4Å:- Chain B: N.657
Ligand excluded by PLIPNAG.37: 1 residues within 4Å:- Chain B: N.343
Ligand excluded by PLIPNAG.38: 2 residues within 4Å:- Chain B: N.164, N.165
Ligand excluded by PLIPNAG.39: 2 residues within 4Å:- Chain B: Y.28, N.61
Ligand excluded by PLIPNAG.40: 2 residues within 4Å:- Chain B: N.603, T.604
Ligand excluded by PLIPNAG.41: 3 residues within 4Å:- Chain B: N.122, T.124, V.127
Ligand excluded by PLIPNAG.42: 2 residues within 4Å:- Chain C: N.616, T.618
Ligand excluded by PLIPNAG.43: 1 residues within 4Å:- Chain C: N.603
Ligand excluded by PLIPNAG.44: 3 residues within 4Å:- Chain C: N.331, I.332, Q.580
Ligand excluded by PLIPNAG.46: 3 residues within 4Å:- Chain C: N.165, T.167
- Chain D: R.357
Ligand excluded by PLIPNAG.49: 4 residues within 4Å:- Chain D: F.338, G.339, N.343, V.367
Ligand excluded by PLIP- 2 x MAN: alpha-D-mannopyranose(Non-functional Binders)
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.47: 4 residues within 4Å:- Chain D: N.343, S.373, F.374, W.436
1 PLIP interactions:1 interactions with chain D- pi-Cation interactions: D:W.436
DMS.48: 3 residues within 4Å:- Chain D: G.404, D.405, Y.508
No protein-ligand interaction detected (PLIP)DMS.50: 5 residues within 4Å:- Chain D: V.382, S.383, K.386, L.387, L.390
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:S.383
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Melero, R. et al., Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj (2020)
- Release Date
- 2020-07-29
- Peptides
- Spike glycoprotein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
BD
a
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 16 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 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
- 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
- 1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x MAN: alpha-D-mannopyranose(Non-functional Binders)
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Melero, R. et al., Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj (2020)
- Release Date
- 2020-07-29
- Peptides
- Spike glycoprotein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
BD
a