- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.20 Å
- Oligo State
- homo-trimer
- Ligands
- 30 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
NAG-NAG.1: 3 residues within 4Å:- Chain A: C.15, N.17, N.137
No protein-ligand interaction detected (PLIP)NAG-NAG.2: 4 residues within 4Å:- Chain A: N.122, A.123, T.124, N.125
No protein-ligand interaction detected (PLIP)NAG-NAG.3: 2 residues within 4Å:- Chain A: N.164, N.165
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 4 residues within 4Å:- Chain A: T.108, N.234, T.236
- Chain C: E.465
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 4 residues within 4Å:- Chain A: N.280, E.281, N.282
- Chain C: K.558
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 2 residues within 4Å:- Chain A: N.331, Q.580
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 4 residues within 4Å:- Chain A: N.616, T.618, Q.644
- Chain B: I.834
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 3 residues within 4Å:- Chain A: N.717, L.922, Q.1071
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.922
NAG-NAG.9: 3 residues within 4Å:- Chain A: N.801, S.803, Q.804
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 1 residues within 4Å:- Chain A: N.1134
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 2 residues within 4Å:- Chain B: N.17, N.137
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.137
NAG-NAG.14: 5 residues within 4Å:- Chain B: N.122, T.124, E.154, E.169, V.171
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.171
NAG-NAG.15: 5 residues within 4Å:- Chain A: R.346, Y.351
- Chain B: E.132, N.164, N.165
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.351
NAG-NAG.16: 3 residues within 4Å:- Chain B: T.108, N.234, T.236
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:T.236
NAG-NAG.17: 3 residues within 4Å:- Chain A: K.558
- Chain B: E.281, N.282
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 2 residues within 4Å:- Chain B: N.331, P.579
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 4 residues within 4Å:- Chain B: N.616, T.618, Q.644
- Chain C: I.834
No protein-ligand interaction detected (PLIP)NAG-NAG.20: 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.21: 3 residues within 4Å:- Chain B: N.801, S.803, Q.804
No protein-ligand interaction detected (PLIP)NAG-NAG.24: 2 residues within 4Å:- Chain B: I.1132, N.1134
No protein-ligand interaction detected (PLIP)NAG-NAG.25: 3 residues within 4Å:- Chain C: C.15, N.17, N.137
No protein-ligand interaction detected (PLIP)NAG-NAG.26: 8 residues within 4Å:- Chain C: N.122, T.124, N.125, V.127, K.129, E.154, E.169, V.171
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.171
NAG-NAG.27: 4 residues within 4Å:- Chain B: Y.351
- Chain C: E.132, N.164, N.165
No protein-ligand interaction detected (PLIP)NAG-NAG.28: 6 residues within 4Å:- Chain B: R.457, K.462, E.465
- Chain C: T.108, N.234, T.236
No protein-ligand interaction detected (PLIP)NAG-NAG.29: 2 residues within 4Å:- Chain C: E.281, N.282
No protein-ligand interaction detected (PLIP)NAG-NAG.30: 1 residues within 4Å:- Chain C: N.331
No protein-ligand interaction detected (PLIP)NAG-NAG.31: 4 residues within 4Å:- Chain A: I.834, Q.836
- Chain C: N.616, T.618
No protein-ligand interaction detected (PLIP)NAG-NAG.32: 4 residues within 4Å:- Chain C: N.717, L.922, Q.926, Q.1071
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.922
NAG-NAG.33: 2 residues within 4Å:- Chain C: N.801, S.803
No protein-ligand interaction detected (PLIP)NAG-NAG.36: 1 residues within 4Å:- Chain C: N.1134
No protein-ligand interaction detected (PLIP)- 3 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: 3 residues within 4Å:- Chain A: A.706, E.1072, N.1074
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.22: 4 residues within 4Å:- Chain B: A.706, E.1072, K.1073, N.1074
No protein-ligand interaction detected (PLIP)NAG-NAG-FUC.34: 2 residues within 4Å:- Chain C: A.706, N.1074
No protein-ligand interaction detected (PLIP)- 3 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN.11: 4 residues within 4Å:- Chain A: N.1098, T.1100, H.1101, F.1103
No protein-ligand interaction detected (PLIP)NAG-NAG-MAN.23: 4 residues within 4Å:- Chain B: N.1098, T.1100, H.1101, F.1103
No protein-ligand interaction detected (PLIP)NAG-NAG-MAN.35: 4 residues within 4Å:- Chain C: N.1098, T.1100, H.1101, F.1103
No protein-ligand interaction detected (PLIP)- 21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
NAG.37: 3 residues within 4Å:- Chain A: F.59, S.60, N.61
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain A: K.147, N.148, N.149
Ligand excluded by PLIPNAG.39: 5 residues within 4Å:- Chain A: F.338, G.339, F.342, N.343, V.367
Ligand excluded by PLIPNAG.40: 1 residues within 4Å:- Chain A: N.603
Ligand excluded by PLIPNAG.41: 2 residues within 4Å:- Chain A: H.655, N.657
Ligand excluded by PLIPNAG.42: 3 residues within 4Å:- Chain A: N.709, G.1131
- Chain B: D.796
Ligand excluded by PLIPNAG.43: 1 residues within 4Å:- Chain A: N.1158
Ligand excluded by PLIPNAG.44: 1 residues within 4Å:- Chain B: N.61
Ligand excluded by PLIPNAG.45: 2 residues within 4Å:- Chain B: N.149, M.153
Ligand excluded by PLIPNAG.46: 4 residues within 4Å:- Chain B: F.338, G.339, F.342, N.343
Ligand excluded by PLIPNAG.47: 1 residues within 4Å:- Chain B: N.603
Ligand excluded by PLIPNAG.48: 1 residues within 4Å:- Chain B: N.657
Ligand excluded by PLIPNAG.49: 3 residues within 4Å:- Chain B: N.709, G.1131
- Chain C: D.796
Ligand excluded by PLIPNAG.50: 1 residues within 4Å:- Chain B: N.1158
Ligand excluded by PLIPNAG.51: 2 residues within 4Å:- Chain C: F.59, N.61
Ligand excluded by PLIPNAG.52: 3 residues within 4Å:- Chain C: K.147, N.148, N.149
Ligand excluded by PLIPNAG.53: 5 residues within 4Å:- Chain C: F.338, F.342, N.343, L.368, S.371
Ligand excluded by PLIPNAG.54: 1 residues within 4Å:- Chain C: N.603
Ligand excluded by PLIPNAG.55: 2 residues within 4Å:- Chain C: H.655, N.657
Ligand excluded by PLIPNAG.56: 2 residues within 4Å:- Chain C: N.709, G.1131
Ligand excluded by PLIPNAG.57: 1 residues within 4Å:- Chain C: N.1158
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, J. et al., Structural impact on SARS-CoV-2 spike protein by D614G substitution. Science (2021)
- Release Date
- 2021-03-24
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.20 Å
- Oligo State
- homo-trimer
- Ligands
- 30 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
- 3 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- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, J. et al., Structural impact on SARS-CoV-2 spike protein by D614G substitution. Science (2021)
- Release Date
- 2021-03-24
- Peptides
- Spike glycoprotein: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C